[R] increasing smoothing in GAMM (package mgcv)
Is there a way in GAMM to increase the amount of smoothing (something like min.sp in GAM)? This is a large-data problem with binomial response. I can get something like the desired effect by using very few knots, but this seems like a kludge. thanks! Scott Olsson [[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] scatterplot3d with categorical data
Dear users, I'm trying to produce a 3d bar plot but the x and y dimensions have categorical data -- so I only want 3 points on each axis. So I try: require(scatterplot3d) mymat-data.frame( x=c(1,1,1,2,2,2,3,3,3), y=c(1,2,3,1,2,3,1,2,3), z=c(1,2,3,4,5,6,7,8,9)) scatterplot3d(mymat, type=h, lwd=5, pch= , xlab=xlabel, ylab=ylabel, zlab=zlabel, xlim=c(1,3), ylim=c(1,3), lab=c(3,3), x.ticklabs=c(Low,Medium,High), y.ticklabs=c(Green,Blue,Black), main=My Bar Plot) But I still get x ticks at 1, 1.5, 2, 2.5, 3 on both x and y axes. I thought lab controlled this (according to the documentation). What am I doing wrong, or is there some restriction on the way the function works? Cheers, Geoff Russell __ 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 subject)
Hi, The following code, from Angelo Canty article on line
Resampling Methods in R: the boot Package, 2002, works fine for Angelo Canty
using R 2.6.0 on Windows XP.
It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after
installing the S-PLUS bootstrap library, with slight differences in my outputs.
library(boot)
library(survival)
set.seed(12345)
mel - melanoma[melanoma$ulcer==1,]
mel$cens - 1*(mel$status==1)
mel.cox - coxph(Surv(time, status==1)~thickness,
+ data=mel)
mel.surv - survfit(mel.cox)
mel.cens - survfit(Surv(time-0.001*(status==1),status!=1)~1,
+ data=mel)
mel.fun - function(d) {
+ cox - coxph(Surv(time, status==1)~thickness,
+ data=d)
+ cox$coefficients}
mel.boot.con - censboot(mel, mel.fun, R=999, sim=cond,
+ F.surv=mel.surv, G.surv=mel.cens,
+ cox=mel.cox, index=c(1,8))
mel.boot.con
CONDITIONAL BOOTSTRAP FOR CENSORED DATA
Call:
censboot(data = mel, statistic = mel.fun, R = 999, F.surv = mel.surv,
G.surv = mel.cens, sim = cond, cox = mel.cox, index = c(1,
8))
Bootstrap Statistics :
original biasstd. error
t1* 0.09967665 0.03579701 0.04973614
I want to apply the Fast bootstrap method from Salibian-Barrera and Zamar
(2003) and Salibian-Barrera, M., Van Aels, S. and Willems, G. (2007) to the
previous example, i.e., to produce a confidence interval for the exponent of
the coefficient of tumour thickness in the Melanoma dataset . Moreover, I
want to compare the performance of the Fast bootstrap with that of the
classical bootstrap, which requires of course computing power and time. How I
can adjust the previous code to do what I want. I asked Angelo Canty for
helping me to do this, but he told me that he is afraid that he does not know
anything about the Fast Bootstrap to which I refer. He suspects that one could
force his boot package to do something like this but he is not sure if that
would be possible through censboot or not. Although my problem does seem
interesting for him, he is afraid that he is not currently in a position to
take on any new collaborations. He remains available to answer any
questions about the boot package itself as it is currently written, he just
does not have the time to consider including new elements into the library at
this time.
I think that the paper of Salibian-barrera and Zamar (2003) is not published
till now. Now I do not have an electronic copy of this paper draft but I have
a hard copy. And so I can send you an attachment including some written
sections from this paper Fast and Stable Bootstrap Methods for Statistics
Defined by Estimating Equations, Salibian-Barrera and Zamar (2003). Please
tell me If you want to send you this attachment, which can also includes what
I want to do, and what I suggest.
I need the adjusted code bad. I hope you help me. If you can not help me,
please guide me to anyone who can help me. Thank you in advance.
Alyaa Mohammad El-wakf
Assistant Lecturer
Department of Applied Statistics and Insurance
Faculty of Commerce
Mansoura University
Egypt
-
[[alternative HTML version deleted]]
__
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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.
[R] Help me to adjust the R code
Hi, The following code, from Angelo Canty article on line Resampling
Methods in R: the boot Package, 2002, works fine for Angelo Canty using R
2.6.0 on Windows XP.
It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after
installing the S-PLUS bootstrap library, with slight differences in my outputs.
library(boot)
library(survival)
set.seed(12345)
mel - melanoma[melanoma$ulcer==1,]
mel$cens - 1*(mel$status==1)
mel.cox - coxph(Surv(time, status==1)~thickness,
+ data=mel)
mel.surv - survfit(mel.cox)
mel.cens - survfit(Surv(time-0.001*(status==1),status!=1)~1,
+ data=mel)
mel.fun - function(d) {
+ cox - coxph(Surv(time, status==1)~thickness,
+ data=d)
+ cox$coefficients}
mel.boot.con - censboot(mel, mel.fun, R=999, sim=cond,
+ F.surv=mel.surv, G.surv=mel.cens,
+ cox=mel.cox, index=c(1,8))
mel.boot.con
CONDITIONAL BOOTSTRAP FOR CENSORED DATA
Call:
censboot(data = mel, statistic = mel.fun, R = 999, F.surv = mel.surv,
G.surv = mel.cens, sim = cond, cox = mel.cox, index = c(1,
8))
Bootstrap Statistics :
original biasstd. error
t1* 0.09967665 0.03579701 0.04973614
I want to apply the Fast bootstrap method from Salibian-Barrera and Zamar
(2003) and Salibian-Barrera, M., Van Aels, S. and Willems, G. (2007) to the
previous example, i.e., to produce a confidence interval for the exponent of
the coefficient of tumour thickness in the Melanoma dataset . Moreover, I
want to compare the performance of the Fast bootstrap with that of the
classical bootstrap, which requires of course computing power and time. How I
can adjust the previous code to do what I want. I asked Angelo Canty for
helping me to do this, but he told me that he is afraid that he does not know
anything about the Fast Bootstrap to which I refer. He suspects that one could
force his boot package to do something like this but he is not sure if that
would be possible through censboot or not. Although my problem does seem
interesting for him, he is afraid that he is not currently in a position to
take on any new collaborations. He remains available to answer any
questions about the boot package itself as it is currently written, he just
does not have the time to consider including new elements into the library at
this time. Salibian-Barrera and Zamar ( 2003) have studied in their paper the
problem of estimating the distribution of statistics defined by estimating
equations. In particular, they have considered two cases: robust regression
estimates and quasi-likelihood estimates.Their approach applies in principle to
the wider class of estimates defined by estimating equations. The Fast
bootstrap povides an inference procedure that is notably faster than the
classical bootstrap (where the estimating equations have to be fully solved for
each bootstrap sample). Salibian-Barrera and Zamar simulation studies have
shown that this Fast bootstrap method is more efficient and more robust to
model departures. I think that the paper of Salibian-barrera and Zamar (2003)
is not published till now. Now I do not have an electronic copy of
this paper draft but I have a hard copy. And so I can send you an attachment
including some written sections from this paper Fast and Stable Bootstrap
Methods for Statistics Defined by Estimating Equations, Salibian-Barrera and
Zamar (2003). Please tell me If you want to send you this attachment, which
can also includes what I want to do, and what I suggest.
I need the adjusted code bad. I hope you help me. If you can not help me,
please guide me to anyone who can help me. Thank you in advance.
Alyaa Mohammad El-wakf
Assistant Lecturer
Department of Applied Statistics and Insurance
Faculty of Commerce
Mansoura University
Egypt
-
[[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] Read stata file from internet?
Dear R-helpers,
I would like to have my students read into R an online Stata dataset:
'http://www.stat.ucla.edu/projects/datasets/risk_project.dta'
I was able to read it into R after downloading it and converting it
with StatTransfer (http://www.stattransfer.com/).
Here is what happens when I use read.dta() as I would use read.table():
require(foreign)
risk2 -
read.dta('http://www.stat.ucla.edu/projects/datasets/risk_project.dta')
Error in
read.dta(http://www.stat.ucla.edu/projects/datasets/risk_project.dta
) :
unable to open file
Then I try:
riskTmp -
read.table('http://www.stat.ucla.edu/projects/datasets/risk_project.dta')
Warning message:
In read.table(http://www.stat.ucla.edu/projects/datasets/risk_project.dta
) :
incomplete final line found by readTableHeader on
'http://www.stat.ucla.edu/projects/datasets/risk_project.dta'
head(riskTmp)
V1
1 l\001\001\300
2.%9.0g
3 \342CNTL%8.0g
risk2 - read.dta(riskTmp)
Error in read.dta(riskTmp) : first argument must be a file name
So I tried to save riskTmp as a file, and read it in using read.dta():
save(riskTmp, file = 'risk.dta')
risk2 - read.dta('risk.dta')
Error in read.dta(risk.dta) : not a Stata version 5-8 .dta file
But that presumably garbled the file. (Indeed, StatTransfer told me so.)
Would it be appropriate to request this as a feature of
foreign::read.dta()? (Thomas Lumley is the author.)
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
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] Who can tell me how I adjust the R code for bootstrapping the Cox model?
Hi,
The following code, from Angelo Canty article on line Resampling Methods in
R: the boot Package, 2002, works fine for Angelo Canty using R 2.6.0 on
Windows XP.
It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after
installing the S-PLUS bootstrap library, with slight differences in my outputs.
library(boot)
library(survival)
set.seed(12345)
mel - melanoma[melanoma$ulcer==1,]
mel$cens - 1*(mel$status==1)
mel.cox - coxph(Surv(time, status==1)~thickness,
+ data=mel)
mel.surv - survfit(mel.cox)
mel.cens - survfit(Surv(time-0.001*(status==1),status!=1)~1,
+ data=mel)
mel.fun - function(d) {
+ cox - coxph(Surv(time, status==1)~thickness,
+ data=d)
+ cox$coefficients}
mel.boot.con - censboot(mel, mel.fun, R=999, sim=cond,
+ F.surv=mel.surv, G.surv=mel.cens,
+ cox=mel.cox, index=c(1,8))
mel.boot.con
CONDITIONAL BOOTSTRAP FOR CENSORED DATA
Call:
censboot(data = mel, statistic = mel.fun, R = 999, F.surv = mel.surv,
G.surv = mel.cens, sim = cond, cox = mel.cox, index = c(1,
8))
Bootstrap Statistics :
original biasstd. error
t1* 0.09967665 0.03579701 0.04973614
I want to apply the Fast bootstrap method from Salibian-Barrera and Zamar
(2003) and Salibian-Barrera, M., Van Aels, S. and Willems, G. (2007) to the
previous example, i.e., to produce a confidence interval for the exponent of
the coefficient of tumour thickness in the Melanoma dataset . Moreover, I
want to compare the performance of the Fast bootstrap with that of the
classical bootstrap, which requires of course computing power and time. How I
can adjust the previous code to do what I want. I asked Angelo Canty for
helping me to do this, but he told me that he is afraid that he does not know
anything about the Fast Bootstrap to which I refer. He suspects that one could
force his boot package to do something like this but he is not sure if that
would be possible through censboot or not. Although my problem does seem
interesting for him, he is afraid that he is not currently in a position to
take on any new collaborations. He remains available to answer any
questions about the boot package itself as it is currently written, he just
does not have the time to consider including new elements into the library at
this time.
I think that the paper of Salibian-barrera and Zamar (2003) is not published
till now. Now I do not have an electronic copy of this paper draft but I have
a hard copy. And so I can send you an attachment including some written
sections from this paper Fast and Stable Bootstrap Methods for Statistics
Defined by Estimating Equations, Salibian-Barrera and Zamar (2003). Please
tell me If you want to send you this attachment, which can also includes what
I want to do, and what I suggest.
I need the adjusted code bad. I hope you help me. If you can not help me,
please guide me to anyone who can help me. Thank you in advance.
Alyaa Mohammad El-wakf
Assistant Lecturer
Department of Applied Statistics and Insurance
Faculty of Commerce
Mansoura University
Egypt
-
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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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] sending the same e-mail many times (was no subject)
Dear Alyaa, you've now sent this message in many different forms to the R-help mailing list. The fact that you did not get a response may very well be related to the way you asked your question, but also that it probably is not an easy question to answer. But sending your e-mail repeatedly to *several thousand* people is considered *very* impolite. aw == alyaa wakf [EMAIL PROTECTED] on Sat, 26 Jan 2008 02:12:25 -0800 (PST) writes: aw Hi, The following code, from Angelo Canty article on line Resampling Methods in R: the boot Package, 2002, works fine for Angelo Canty using R 2.6.0 on Windows XP. aw It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after installing the S-PLUS bootstrap library, with slight differences in my outputs. [.] the footer here tells us that you still don't follow the posting guide (namely, not sending HTML) even though you may have started doing so by trying to produce reproducible code. Regards, Martin Maechler, ETH Zurich aw - aw [[alternative HTML version deleted]] aw __ aw R-help@r-project.org mailing list aw https://stat.ethz.ch/mailman/listinfo/r-help aw PLEASE do read the posting guide http://www.R-project.org/posting-guide.html aw 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] using facet_grid() from ggplot2 with additional text in labels
Hi I am using ggplot2 at the moment and I must say it is definitely better then ggplot - good work. My problem is that I am using facet_grid() in the following way: p - ggplot(ssq, aes(x=year, y=-log(ssq))) p + geom_point() + facet_grid(me*gi~cs*rz) and it works nicely, except that I would like to have, in naddition to the values of me, gi, cs and rz the name of the variable. I.e: if gi is 1, 2 and 3 I would like to have gi = 1:, gi = 2 and gi = 3 as labels of the p[anels. I did it with ggplot, but I don't remember and I have lost the code ... Just a small comment on the package: as I am using emacs with ess, I have to press _ twice to get the underscore in the commands (as the first one is replaced with - and then reverted to _) - would it be possible to change these in the next release with . (but still provide an alias with _)? Thanks a lot Rainer __ 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.
Newsletter: Vielen dank f�r ihre Anmeldung!
Hallo, Ihre E-Mailadresse [EMAIL PROTECTED] wurde in den Newsletterverteiler hinzugefügt. URL: http://www.fueralles.de/cgi-bin/nsl_pro/newsletter.cgi?id=steinfeuerfred Mit freundlichen Grüssen Ihr Newsletter-Team __ 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] rowsum- is there a countsum
Hello Is there an analogous function to ”rowsum” that count the numbers according to a given vector (preferably larger than a given value) instead of summing them? E.g. rowsum(x, group) X is the dataframe, A B C 5 0 0 1 3 3 0 1 12 and group is the vector; 1,1,2 rowsum gives: A B C 1 6 3 3 2 0 1 12 I want: A B C 1 2 1 1 2 0 1 1 for e.g. count all 0. Best Regards Anders __ 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] Capturing info from system calls in Windows
Colleagues, I am preparing scripts that will be used by others on both Windows and Linux/OSX platforms. The scripts call an existing Fortran application. The user may have any of a a variety of Fortran compilers - my goal is to determine whether or not the test command returns no input files or command not found (i.e., so that I can confirm which Fortran they are using). In OS X and Linux, I can do the following: TEST - system(g77 21, intern=TRUE) TEST [1] g77: no input files TEST - system(f77 21, intern=TRUE) TEST [1] sh: f77: command not found I can then use grep to determine which of the two strings was returned. In Windows: TEST - system(g95 21) g95: 21: Invalid argument TEST [1] 0 attr(, exec.status): [1] 0 attr(, exit.status): [1] 0 TEST - system(g95) g95: no input files TEST [1] 0 attr(, exec.status): [1] 0 attr(, exit.status): [1] 0 As you can see, Windows replies no input files; however, that info is not captured in TEST. I presume that this is because standard error is dealt with different in Windows compared to Unix-line platforms. Any thoughts on how to capture standard error in Windows? Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.com [[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] rowsum- is there a countsum
Is this what you are looking for in doing computations on the columns of a dataframe? x - data.frame(group=sample(1:2,10,TRUE),A=sample(1:4,10,TRUE),B=sample(1:5,10,TRUE), + C=sample(1:3,10,TRUE)) x group A B C 1 1 2 4 1 2 2 4 1 2 3 1 3 2 1 4 2 3 2 2 5 2 4 2 2 6 1 2 5 1 7 2 1 5 2 8 1 1 5 3 9 1 4 3 2 10 2 2 1 1 # sum in each column aggregate(x[,-1], list(x$group), sum) Group.1 A B C 1 1 12 19 8 2 2 14 11 9 # count greater than 2 aggregate(x[,-1], list(x$group),function(.col) sum(.col2)) Group.1 A B C 1 1 2 4 1 2 2 3 1 0 On Jan 26, 2008 9:13 AM, Anders Bjørgesæter [EMAIL PROTECTED] wrote: Hello Is there an analogous function to rowsum that count the numbers according to a given vector (preferably larger than a given value) instead of summing them? E.g. rowsum(x, group) X is the dataframe, A B C 5 0 0 1 3 3 0 1 12 and group is the vector; 1,1,2 rowsum gives: A B C 1 6 3 3 2 0 1 12 I want: A B C 1 2 1 1 2 0 1 1 for e.g. count all 0. Best Regards Anders __ 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? __ 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] Capturing info from system calls in Windows
On 26/01/2008 9:17 AM, Dennis Fisher wrote: Colleagues, I am preparing scripts that will be used by others on both Windows and Linux/OSX platforms. The scripts call an existing Fortran application. The user may have any of a a variety of Fortran compilers - my goal is to determine whether or not the test command returns no input files or command not found (i.e., so that I can confirm which Fortran they are using). In OS X and Linux, I can do the following: TEST - system(g77 21, intern=TRUE) TEST [1] g77: no input files TEST - system(f77 21, intern=TRUE) TEST [1] sh: f77: command not found I can then use grep to determine which of the two strings was returned. In Windows: TEST - system(g95 21) g95: 21: Invalid argument TEST [1] 0 attr(, exec.status): [1] 0 attr(, exit.status): [1] 0 TEST - system(g95) g95: no input files TEST [1] 0 attr(, exec.status): [1] 0 attr(, exit.status): [1] 0 As you can see, Windows replies no input files; however, that info is not captured in TEST. I presume that this is because standard error is dealt with different in Windows compared to Unix-line platforms. Any thoughts on how to capture standard error in Windows? See ?system. You want intern=TRUE there, too. system(gcc) gcc.exe: no input files system(gcc, intern=TRUE) [1] gcc.exe: no input files Duncan Murdoch Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.com [[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] how to use anova() to test the sum of coefficients in nlme package
Dear R-help, In nlme package, anova () can be used to test the difference between two coefficients as shown on page 225 of Mixed Effects Models in S and S-Plus: anova(fm2BW.lme, L = c(Time:Diet2 = 1, Time:Diet3 = -1)) Now my question is instead of test the difference between two coefficients, can I use anova to test the significance of the sum of two coefficients, like anova(fm2BW.lme, L = c(Time:Diet2 = 1, Time:Diet3 = 1)) Thanks, Shirley __ 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] Which R version created a package?
Greetings, R-ians: I would like to know which version or R was used to create a given package. I think I remember seeing that topic discussed recently but cannot find it among my notes. Can anyone tell me how to determine which version of R created a package? Thanks. Charles Annis, P.E. mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com http://www.StatisticalEngineering.com [[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] Which R version created a package?
library(help=lattice) [...] Built: R 2.6.0; i486-pc-linux-gnu; 2008-01-23 13:52:49; unix [...] G. On Sat, Jan 26, 2008 at 11:44:53AM -0500, Charles Annis, P.E. wrote: Greetings, R-ians: I would like to know which version or R was used to create a given package. I think I remember seeing that topic discussed recently but cannot find it among my notes. Can anyone tell me how to determine which version of R created a package? Thanks. Charles Annis, P.E. mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com http://www.StatisticalEngineering.com [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Which R version created a package?
These also works should you need to capture it: packageDescription(lattice)$Built On Jan 26, 2008 12:04 PM, Gabor Csardi [EMAIL PROTECTED] wrote: library(help=lattice) [...] Built: R 2.6.0; i486-pc-linux-gnu; 2008-01-23 13:52:49; unix [...] G. On Sat, Jan 26, 2008 at 11:44:53AM -0500, Charles Annis, P.E. wrote: Greetings, R-ians: I would like to know which version or R was used to create a given package. I think I remember seeing that topic discussed recently but cannot find it among my notes. Can anyone tell me how to determine which version of R created a package? Thanks. Charles Annis, P.E. mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com http://www.StatisticalEngineering.com [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Which R version created a package?
On 26/01/2008 11:44 AM, Charles Annis, P.E. wrote: Greetings, R-ians: I would like to know which version or R was used to create a given package. I think I remember seeing that topic discussed recently but cannot find it among my notes. Can anyone tell me how to determine which version of R created a package? You can see which version was used to build the package by looking in the DESCRIPTION file; that information is available in R via something like packageDescription(graphics, fields=Built) Duncan Murdoch Thanks. Charles Annis, P.E. mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com http://www.StatisticalEngineering.com [[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] scatterplot3d with categorical data
hits=-2.6 tests=BAYES_00 X-USF-Spam-Flag: NO Dear Geoff, scatterplot3d was never intended to draw a plot for categorical data, but you can tweak it as follows: - Note that the help page says (stolen from ?par) The values of x and y give the (approximate) number of tickmarks on the x and y axes. where approximate is stressed in this context. It works for me to use lab = c(2,2) - add argument mar = c(3,3,3,3) - add argument y.margin.add = 0.15, Best, Uwe Geoff Russell wrote: Dear users, I'm trying to produce a 3d bar plot but the x and y dimensions have categorical data -- so I only want 3 points on each axis. So I try: require(scatterplot3d) mymat-data.frame( x=c(1,1,1,2,2,2,3,3,3), y=c(1,2,3,1,2,3,1,2,3), z=c(1,2,3,4,5,6,7,8,9)) scatterplot3d(mymat, type=h, lwd=5, pch= , xlab=xlabel, ylab=ylabel, zlab=zlabel, xlim=c(1,3), ylim=c(1,3), lab=c(3,3), x.ticklabs=c(Low,Medium,High), y.ticklabs=c(Green,Blue,Black), main=My Bar Plot) But I still get x ticks at 1, 1.5, 2, 2.5, 3 on both x and y axes. I thought lab controlled this (according to the documentation). What am I doing wrong, or is there some restriction on the way the function works? Cheers, Geoff Russell __ 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] Which R version created a package?
Many thanks to all. These methods all provide the needed info: library(help= lattice) packageDescription(lattice , fields=Built) packageDescription(lattice)$Built The first method produces nore complete information, should that also be interesting. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gabor Csardi Sent: Saturday, January 26, 2008 12:05 PM To: Charles Annis, P.E. Cc: 'RHelp' Subject: Re: [R] Which R version created a package? library(help=lattice) [...] Built: R 2.6.0; i486-pc-linux-gnu; 2008-01-23 13:52:49; unix [...] G. On Sat, Jan 26, 2008 at 11:44:53AM -0500, Charles Annis, P.E. wrote: Greetings, R-ians: I would like to know which version or R was used to create a given package. I think I remember seeing that topic discussed recently but cannot find it among my notes. Can anyone tell me how to determine which version of R created a package? Thanks. Charles Annis, P.E. mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com http://www.StatisticalEngineering.com [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] interactive menu in scripts
Hi, Not going into the reason why would you like to do such a thing anyway, I would suggest: 1. Creating an R file that would contain all the functionality coded in functions. 2. The only executed code would be a function that calls the menu() and executes the appropriate functions. Sources of existing packages provide a good reference. Have a look for example on the sources of plot.eff.list in the package 'effects'. HTH, Michal Sources of existing packa WCD wrote: Hello, I would like to make my R script more interactive. Well, I want the script to work like this: I run the script from R Console and it offers me some options (press 1 for something, or press 2 for something else). After pressing 1 or 2, do corresponding procedure. I am not able to find out how to do this. I guess the functions menu() or switch() are the keys, but I didn't manage to use them properly. Can you help me? Are there some more practical examples on the web? Tahnks, Filip Kral. - Michal Bojanowski ICS / Department of Sociology Utrecht University Heidelberglaan 2; 3584 CS Utrecht The Netherlands m.j.bojanowski at uu dot nl http://www.fss.uu.nl/soc/bojanowski/ http://bojan.3e.pl/ -- View this message in context: http://www.nabble.com/interactive-menu-in-scripts-tp15095049p15110587.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] interactive menu in scripts
Try like this: switch(menu(c(Normal, Poisson)), rnorm(5), rpois(5, 3)) On 25/01/2008, WCD [EMAIL PROTECTED] wrote: Hello, I would like to make my R script more interactive. Well, I want the script to work like this: I run the script from R Console and it offers me some options (press 1 for something, or press 2 for something else). After pressing 1 or 2, do corresponding procedure. I am not able to find out how to do this. I guess the functions menu() or switch() are the keys, but I didn't manage to use them properly. Can you help me? Are there some more practical examples on the web? Tahnks, Filip Kral. -- View this message in context: http://www.nabble.com/interactive-menu-in-scripts-tp15095049p15095049.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 __ 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] Function for translation of a list into a matrix as used by ordination?
Try this also: noquote(tapply(x$Abundance, list(x$Plot, x$Species), paste)) On 25/01/2008, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hello. Does anyone know of an existing function that takes a list in the form of: Plot1 Species1Abundance1 Plot1 Species2Abundance2 Plot2 Species1Abundance1 Plot2 Species3Abundance3 . . . PlotN SpeciesNAbundanceN and translates into a matrix in the form of Species1Species2 SpeciesN Plot1 Abundance1 Abundance2... AbundanceN Plot2 Abundance1 Abundance2... AbundanceN . . . PlotN AbundanceN AbundanceN... AbundanceN This is a basic operation used in the initial stages of ordination etc of ecological data (vegetation or other species) that is usually stored in a database or flatfile in the list format above. It is similar to a cross tabulation like the function xtabs(), however its useful to be able to control whether a measured abundance for a taxa is included or a boolean (presence/absence) for the taxa in a given plot. Im new to such analyses in R, but before writing it myself hope or suspect that such a function or library is out there (although I dont see it after some quick searching in things like Vegan or BiodivesityR or labdsv). Thanks billy __ 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 __ 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] double-click in RData file versus load( file )
On 26/01/2008 1:01 PM, Cleber Nogueira Borges wrote:
hello all,
when I start up the R and I execute o follow code:
ls()
character(0)
x=123
assign(test_x, x, envir = .GlobalEnv )
ls()
[1] test_x x
setwd('C:\\R\\etc')
save.image('TEST.RData')
q('no')
I have two different behaviours:
(a) - when I start up R again by double click in the file TEST.RData;
(b) - when I start up R and load the file TEST.RData by window menu in
Rgui or
invoke by command ' load('C:\\R\\etc\\TEST.RData')
In case (a): I can't see my previous variables anymore!
Which version of R are you using? It works fine for me in 2.6.1.
What do you see when R starts? It should display something like
R version 2.6.1 (2007-11-26)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
and the last line indicates the attempt to load the saved data.
Duncan Murdoch
ls()
character(0)
In case (b): I get my previous variables again!
load('C:\\R\\etc\\test.rdata')
ls()
[1] test_x x
Is it the correct behaviour?
the two way don't must be the same?
Thank for explanations...
Cleber Borges
___
Experimente já e veja as novidades.
__
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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.
__
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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.
[R] tutorial specific for R + unix
dear all, is there a tutorial specifically teaching how to use R under unix? it seems most of them are about using r under window. thank you so much! __ 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] Any numeric differentiation routine in R for boundary points?
Hi, I have a scalar valued function with several variables. One of the variables is restricted to be non-negative. For example, f(x,y)=sqrt(x)*exp(y), then x should be non-negative. I need the gradient and hessian for some vector (0,y), i.e., I need the gradient and hessian at the boudary of parameter space. The numderiv package does not work, even for f(x)=sqrt(x), if you do genD(f,x=0), warning message comes out. I need the one sided derivatives. Thanks if you could provide some help. -- View this message in context: http://www.nabble.com/Any-numeric-differentiation-routine-in-R-for-boundary-points--tp15110811p15110811.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] double-click in RData file versus load( file )
When you double click it does it start up the same version of R
as when you manually start R?
If you manually start R, load it, save it under another name and
then exit R and double click the new name does that work?
On Jan 26, 2008 1:01 PM, Cleber Nogueira Borges [EMAIL PROTECTED] wrote:
hello all,
when I start up the R and I execute o follow code:
ls()
character(0)
x=123
assign(test_x, x, envir = .GlobalEnv )
ls()
[1] test_x x
setwd('C:\\R\\etc')
save.image('TEST.RData')
q('no')
I have two different behaviours:
(a) - when I start up R again by double click in the file TEST.RData;
(b) - when I start up R and load the file TEST.RData by window menu in
Rgui or
invoke by command ' load('C:\\R\\etc\\TEST.RData')
In case (a): I can't see my previous variables anymore!
ls()
character(0)
In case (b): I get my previous variables again!
load('C:\\R\\etc\\test.rdata')
ls()
[1] test_x x
Is it the correct behaviour?
the two way don't must be the same?
Thank for explanations...
Cleber Borges
___
Experimente já e veja as novidades.
__
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] Read stata file from internet?
Try this:
tmpfile - tempfile()
download.file('http://www.stat.ucla.edu/projects/datasets/risk_project.dta',
tmpfile)
risk2 - read.dta(tmpfile)
unlink(tmpfile)
On 26/01/2008, Michael Kubovy [EMAIL PROTECTED] wrote:
Dear R-helpers,
I would like to have my students read into R an online Stata dataset:
'http://www.stat.ucla.edu/projects/datasets/risk_project.dta'
I was able to read it into R after downloading it and converting it
with StatTransfer (http://www.stattransfer.com/).
Here is what happens when I use read.dta() as I would use read.table():
require(foreign)
risk2 -
read.dta('http://www.stat.ucla.edu/projects/datasets/risk_project.dta')
Error in
read.dta(http://www.stat.ucla.edu/projects/datasets/risk_project.dta
) :
unable to open file
Then I try:
riskTmp -
read.table('http://www.stat.ucla.edu/projects/datasets/risk_project.dta')
Warning message:
In read.table(http://www.stat.ucla.edu/projects/datasets/risk_project.dta
) :
incomplete final line found by readTableHeader on
'http://www.stat.ucla.edu/projects/datasets/risk_project.dta'
head(riskTmp)
V1
1 l\001\001\300
2.%9.0g
3 \342CNTL%8.0g
risk2 - read.dta(riskTmp)
Error in read.dta(riskTmp) : first argument must be a file name
So I tried to save riskTmp as a file, and read it in using read.dta():
save(riskTmp, file = 'risk.dta')
risk2 - read.dta('risk.dta')
Error in read.dta(risk.dta) : not a Stata version 5-8 .dta file
But that presumably garbled the file. (Indeed, StatTransfer told me so.)
Would it be appropriate to request this as a feature of
foreign::read.dta()? (Thomas Lumley is the author.)
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
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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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
__
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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] interactive menu in scripts
Yes, the switch function works fine.
To store generated values in some variable I just use:
switch(menu(c(Normal, Uniform)), a-rnorm(5), a-runif(5))
But why does not work this? (I know there is waste of variables, but in
principle):
b-numeric(10)
switch(menu(c(Normal, Uniform)), a-1, a-2)
if(a==1) {b-rnorm(10)} else {b-runif(10)}
When I run these commands from a script, the choice is offered after the
condition is performed, so b stores ten zeros.
Also readline() function seems to be what I am looking for. But I did not
manage to use it for my reason; this does not work too:
var-numeric(5)
rdf-function() {
x-readline(Enter 1 for normal, 2 for uniform distribution )
if (x==1) {var-rnorm(5)} else {var-runif(5)}
}
rdf()
Even this does not work (object x is not found):
rdf2-function() {
x-readline(enter your year of birth )
}
rdf2()
Can you see what am I doing wrong?
Anyway, I am sorry for my maybe bizzar explanations. I am quitr new to R and
R forum.
My aim is to write an R script, where the user can make some choices or set
some parameters via the R console. Filip Kral.
Henrique Dallazuanna wrote:
Try like this:
switch(menu(c(Normal, Poisson)), rnorm(5), rpois(5, 3))
On 25/01/2008, WCD [EMAIL PROTECTED] wrote:
__
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
__
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.
--
View this message in context:
http://www.nabble.com/interactive-menu-in-scripts-tp15095049p15111894.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
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Re: [R] tutorial specific for R + unix
Hello, On 1/26/08, Wensui Liu [EMAIL PROTECTED] wrote: dear all, is there a tutorial specifically teaching how to use R under unix? it seems most of them are about using r under window. thank you so much! What exactly are you interested in: installing or using R? If it is the latter, R is remarkably similar on all platforms it runs on. As for the tutorials, you might be interested in these introductory (progressively more advanced) materials [1], [2] and [3]. Liviu [1] http://oit.utk.edu/scc/RforSASSPSSusers.pdf [2] http://zoonek2.free.fr/UNIX/48_R/all.html [3] http://cran.at.r-project.org/doc/contrib/Farnsworth-EconometricsInR.pdf __ 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] An R clause to bind dataframes under certain contions
Hi netters, Suppose I have two data frames X and Y. X has three colnames A, B and C. Y has three colnames A,B and D. I want to combine them into one matrix, joining the rows having the same A and B values (X$A==Y$A and X$B = Y$B). So the resulting dataframe has four variables/columns: A,B,C and D. I was wondering what's the best way to do it in R. Could anyone give me some advice? Thanks! Zhihua Li _ ÊÖ»úÒ²ÄÜÉÏ MSN ÁÄÌìÁË£¬¿ìÀ´ÊÔÊÔ°É£¡ [[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] Read stata file from internet?
Henrique Dallazuanna wrote:
Try this:
tmpfile - tempfile()
download.file('http://www.stat.ucla.edu/projects/datasets/risk_project.dta',
tmpfile)
risk2 - read.dta(tmpfile)
unlink(tmpfile)
The stata.get function in the Hmisc package will automatically fetch
from http://... and provides other features such as conversion of dates
and using variable labels.
Frank
On 26/01/2008, Michael Kubovy [EMAIL PROTECTED] wrote:
Dear R-helpers,
I would like to have my students read into R an online Stata dataset:
'http://www.stat.ucla.edu/projects/datasets/risk_project.dta'
I was able to read it into R after downloading it and converting it
with StatTransfer (http://www.stattransfer.com/).
Here is what happens when I use read.dta() as I would use read.table():
require(foreign)
risk2 -
read.dta('http://www.stat.ucla.edu/projects/datasets/risk_project.dta')
Error in
read.dta(http://www.stat.ucla.edu/projects/datasets/risk_project.dta
) :
unable to open file
Then I try:
riskTmp -
read.table('http://www.stat.ucla.edu/projects/datasets/risk_project.dta')
Warning message:
In read.table(http://www.stat.ucla.edu/projects/datasets/risk_project.dta
) :
incomplete final line found by readTableHeader on
'http://www.stat.ucla.edu/projects/datasets/risk_project.dta'
head(riskTmp)
V1
1 l\001\001\300
2.%9.0g
3 \342CNTL%8.0g
risk2 - read.dta(riskTmp)
Error in read.dta(riskTmp) : first argument must be a file name
So I tried to save riskTmp as a file, and read it in using read.dta():
save(riskTmp, file = 'risk.dta')
risk2 - read.dta('risk.dta')
Error in read.dta(risk.dta) : not a Stata version 5-8 .dta file
But that presumably garbled the file. (Indeed, StatTransfer told me so.)
Would it be appropriate to request this as a feature of
foreign::read.dta()? (Thomas Lumley is the author.)
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
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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.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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Re: [R] tutorial specific for R + unix
dear liviu, first of all, i appreciate your insight. i've been used r on windows for years and might use it on unix. i understand r is similar across OSs. However, per my understanding, still there is nontrivial difference between running on unix and running on windows. have a nice weekend. On Jan 26, 2008 2:43 PM, Liviu Andronic [EMAIL PROTECTED] wrote: Hello, On 1/26/08, Wensui Liu [EMAIL PROTECTED] wrote: dear all, is there a tutorial specifically teaching how to use R under unix? it seems most of them are about using r under window. thank you so much! What exactly are you interested in: installing or using R? If it is the latter, R is remarkably similar on all platforms it runs on. As for the tutorials, you might be interested in these introductory (progressively more advanced) materials [1], [2] and [3]. Liviu [1] http://oit.utk.edu/scc/RforSASSPSSusers.pdf [2] http://zoonek2.free.fr/UNIX/48_R/all.html [3] http://cran.at.r-project.org/doc/contrib/Farnsworth-EconometricsInR.pdf -- === WenSui Liu Statistical Project Manager ChoicePoint Precision Marketing (http://spaces.msn.com/statcompute/blog) __ 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] An R clause to bind dataframes under certain contions
Try this: merge(x, y, all=T) On 26/01/2008, zhihuali [EMAIL PROTECTED] wrote: Hi netters, Suppose I have two data frames X and Y. X has three colnames A, B and C. Y has three colnames A,B and D. I want to combine them into one matrix, joining the rows having the same A and B values (X$A==Y$A and X$B = Y$B). So the resulting dataframe has four variables/columns: A,B,C and D. I was wondering what's the best way to do it in R. Could anyone give me some advice? Thanks! Zhihua Li _ 手机也能上 MSN 聊天了，快来试试吧！ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] An R clause to bind dataframes under certain contions
Hi, Huali, there is another way to do so library(sqldf) wanted - sqldf(select * from X inner join Y on X.A = Y.A and X.B = Y.A) 2008/1/26 zhihuali [EMAIL PROTECTED]: Hi netters, Suppose I have two data frames X and Y. X has three colnames A, B and C. Y has three colnames A,B and D. I want to combine them into one matrix, joining the rows having the same A and B values (X$A==Y$A and X$B = Y$B). So the resulting dataframe has four variables/columns: A,B,C and D. I was wondering what's the best way to do it in R. Could anyone give me some advice? Thanks! Zhihua Li _ 手机也能上 MSN 聊天了，快来试试吧！ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === WenSui Liu Statistical Project Manager ChoicePoint Precision Marketing (http://spaces.msn.com/statcompute/blog) === __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to apply the wilcox_test function to subsets ?
Dear R-forumites,
I want to apply a Wilcoxon test on subsets of the data frame mydata,
splitted using the myindice variable. When I send :
wilcoxtest - by(mydata, mydata$myindice, function(x)
{wilcox_test(x$value~x$fact)})
I get :
Error in eval(expr, envir, enclos) : object x not found
whereas
wilcoxtest - by(mydata, mydata$myindice, function(x)
{wilcox.test(x$value~x$fact)})
works !
Why does it fail with the wilcox_test only? And, most important, how can I
apply the wilcox_test function to subsets of mydata splitted according to
mydata$myindice ?
Thanks in advance,
Jean-Luc Dupouey
Forest Ecology and Ecophysiology Unit
INRA
54280 Champenoux
France
mail: [EMAIL PROTECTED]
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] An R clause to bind dataframes under certain contions
Henrique Dallazuanna [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Try this: merge(x, y, all=T) That will give NA's in the non-matching rows, which may be what the OP wanted. If, on the otherhand, only the rows with matches were desired, the usage might be: A.B - merge(X, Y, by = c(A,B)) A.B mymat-data.frame( x=c(1,1,1,2,2,2,3,3,3), y=c(1,2,3,1,2,3,1,2,3), z=c(1,2,3,4,5,6,7,8,9)) mymat2-data.frame( x=c(1,1,1,2,2,2,3,3,3), y=c(1,2,3,1,2,3,1,4,3), zz=c(1,7,3,5,5,6,10,8,20)) mymerge1 - merge(mymat, mymat2, all=TRUE) mymerge1 x y z zz 1 1 1 1 1 2 1 2 2 7 3 1 3 3 3 4 2 1 4 5 5 2 2 5 5 6 2 3 6 6 7 3 1 7 10 8 3 2 8 NA 9 3 3 9 20 10 3 4 NA 8 mymerge2 - merge(mymat, mymat2, by=c(x,y)) mymerge2 x y z zz 1 1 1 1 1 2 1 2 2 7 3 1 3 3 3 4 2 1 4 5 5 2 2 5 5 6 2 3 6 6 7 3 1 7 10 8 3 3 9 20 -- David Winsemius On 26/01/2008, zhihuali [EMAIL PROTECTED] wrote: Hi netters, Suppose I have two data frames X and Y. X has three colnames A, B and C. Y has three colnames A,B and D. I want to combine them into one matrix, joining the rows having the same A and B values (X$A==Y$A and X$B = Y$B). So the resulting dataframe has four variables/columns: A,B,C and D. I was wondering what's the best way to do it in R. Could anyone give me some advice? Thanks! Zhihua Li __ 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] An R clause to bind dataframes under certain contions
On 26/01/2008, David Winsemius [EMAIL PROTECTED] wrote: Henrique Dallazuanna [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Try this: merge(x, y, all=T) That will give NA's in the non-matching rows, which may be what the OP wanted. If, on the otherhand, only the rows with matches were desired, the usage might be: In this case omit 'all' argument. mymerge1 - merge(mymat, mymat2) A.B - merge(X, Y, by = c(A,B)) A.B mymat-data.frame( x=c(1,1,1,2,2,2,3,3,3), y=c(1,2,3,1,2,3,1,2,3), z=c(1,2,3,4,5,6,7,8,9)) mymat2-data.frame( x=c(1,1,1,2,2,2,3,3,3), y=c(1,2,3,1,2,3,1,4,3), zz=c(1,7,3,5,5,6,10,8,20)) mymerge1 - merge(mymat, mymat2, all=TRUE) mymerge1 x y z zz 1 1 1 1 1 2 1 2 2 7 3 1 3 3 3 4 2 1 4 5 5 2 2 5 5 6 2 3 6 6 7 3 1 7 10 8 3 2 8 NA 9 3 3 9 20 10 3 4 NA 8 mymerge2 - merge(mymat, mymat2, by=c(x,y)) mymerge2 x y z zz 1 1 1 1 1 2 1 2 2 7 3 1 3 3 3 4 2 1 4 5 5 2 2 5 5 6 2 3 6 6 7 3 1 7 10 8 3 3 9 20 -- David Winsemius On 26/01/2008, zhihuali [EMAIL PROTECTED] wrote: Hi netters, Suppose I have two data frames X and Y. X has three colnames A, B and C. Y has three colnames A,B and D. I want to combine them into one matrix, joining the rows having the same A and B values (X$A==Y$A and X$B = Y$B). So the resulting dataframe has four variables/columns: A,B,C and D. I was wondering what's the best way to do it in R. Could anyone give me some advice? Thanks! Zhihua Li __ 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 __ 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] double-click in RData file versus load( file )
hello Gabor, the result in combobox is: R version 2.6.1 (2007-11-26) - C:\R I not have Perl installed! I remember that I deleted it! Just double click on Rversions.hta from Windows Explorer. Alternately place it anywhere in your path and then enter its name in the Windows console without arguments: Rversions.hta Rversions.bat and all the other utilities wor the same way. Neither Rversions.hta nor any of the other programs require that you be in the R directory and, in fact, its probably better that you are not since if you are then it ignores the registry and assumes the version of R you are in is your current version. Rfind.bat could not find Perl. It looks in a few common places. Its still possible you have Perl installed but its not in the places it knows about. There is some info in the README also at http://batchfiles.googlecode.com ___ Experimente já e veja as novidades. __ 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] double-click in RData file versus load( file )
OK. The system only knows about one R version. What about the answer to my original second question. If you start up R and then load the .Rdata file (which you previously indicated works) and then save your workspace using a different name from the original Rdata file and then double click on that new Rdata file does that get you the variables in the new Rdata file? On Jan 26, 2008 4:23 PM, Cleber Nogueira Borges [EMAIL PROTECTED] wrote: hello Gabor, the result in combobox is: R version 2.6.1 (2007-11-26) - C:\R I not have Perl installed! I remember that I deleted it! Just double click on Rversions.hta from Windows Explorer. Alternately place it anywhere in your path and then enter its name in the Windows console without arguments: Rversions.hta Rversions.bat and all the other utilities wor the same way. Neither Rversions.hta nor any of the other programs require that you be in the R directory and, in fact, its probably better that you are not since if you are then it ignores the registry and assumes the version of R you are in is your current version. Rfind.bat could not find Perl. It looks in a few common places. Its still possible you have Perl installed but its not in the places it knows about. There is some info in the README also at http://batchfiles.googlecode.com ___ Yahoo! Mail - Sempre a melhor opção para você! Experimente já e veja as novidades. http://br.yahoo.com/mailbeta/tudonovo/ __ 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-pkgs] RSQLite 0.6-7 -- changes to dbGetQuery semantics
RSQLite 0.6-7 has been uploaded to CRAN and should hit a mirror near you in the next few days. This version changes the behavior of the dbGetQuery method to make it more consistent with dbSendQuery. Specifically: 1. dbGetQuery now closes a complete result set as dbSendQuery does. 2. If there is an incomplete result set open, dbGetQuery still opens a new temporary connection, but now issues a warning. It is best practice to explicitly close open result sets before issuing further queries. These changes are in response to the following discussion on the r-sig-db list: https://stat.ethz.ch/pipermail/r-sig-db/2008q1/000399.html + seth -- Seth Falcon | [EMAIL PROTECTED] | blog: http://userprimary.net/user/ ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] Error: C stack usage is too close to the limit
Lately R has been behaving strange on my Linux (Ubuntu 7.10) machine,
with occasional segfaults. Today something else and reproducible
happened:
If I type the code below (meant for calibrating data), I get the error
message that the C stack usage is too close to the limit.
calcurve - cbind(1:2e4, 1:2e4, 1:2e3); #dummy curve, real one is more complex
caldist - function(cage=Cage, error=Error, sdev=Sdev, times=Times, By=By)
{
theta - seq(min(calcurve[,1]), max(calcurve[,1]), by=By);
interpolate - function(th, col)
{
if(th==calcurve[1,1]) {calcurve[1,col]}else
if(th==calcurve[nrow(calcurve),1]) {calcurve[nrow(calcurve),col]}else
{
k - min(which(calcurve[,1] th));
slope -
(calcurve[k-1,col]-calcurve[k,col])/(calcurve[k-1,1]-calcurve[k,1]);
calcurve[k-1,col] + slope*(th-calcurve[k-1,1]);
}
}
mu - c();
cerror - c();
for(i in 1:length(theta))
{
mu[i] - interpolate(theta[i],2);
cerror[i] - interpolate(theta[i],3);
}
caldist - dnorm(mu, cage, (error^2+cerror^2)^.5);
cbind(theta, caldist/sum(caldist));
}
caldist(1e3,1e2);
Unfortunately I am no huge computer wizard. Has anyone got any idea
why this happens? Is it reproducible on other machines? How can I
solve this problem?
My R:
R version 2.6.1 (2007-11-26)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
Cstack_info()
sizecurrent direction eval_depth
8388608 2404 1 2
Many thanks,
Maarten Blaauw
--
Dr. Maarten Blaauw
School of Geography, Archaeology Palaeoecology
Queen's University Belfast, U.K.
On leave from Department of Earth Sciences
Uppsala University, Sweden
[EMAIL PROTECTED]
__
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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] double-click in RData file versus load( file )
hi, I tried this approach, but don't work too! (Duncan Murdoch make this suggestion) Cleber OK. The system only knows about one R version. What about the answer to my original second question. If you start up R and then load the .Rdata file (which you previously indicated works) and then save your workspace using a different name from the original Rdata file and then double click on that new Rdata file does that get you the variables in the new Rdata file? ___ Experimente já e veja as novidades. __ 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] An R clause to bind dataframes under certain contions
Have a look at rbind.fill() in the reshape library. This will return a data.frame not a matrix but you can always convert it to a matrix. --- zhihuali [EMAIL PROTECTED] wrote: Hi netters, Suppose I have two data frames X and Y. X has three colnames A, B and C. Y has three colnames A,B and D. I want to combine them into one matrix, joining the rows having the same A and B values (X$A==Y$A and X$B = Y$B). So the resulting dataframe has four variables/columns: A,B,C and D. I was wondering what's the best way to do it in R. Could anyone give me some advice? Thanks! Zhihua Li _ ÊÖ»úÒ²ÄÜÉÏ MSN ÁÄÌìÁË£¬¿ìÀ´ÊÔÊÔ°É£¡ [[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] double-click in RData file versus load( file )
Gabor Grothendieck wrote: Please clarify. What happens? ok! I start up the R, load my file by win menu: Load Workspace, ls() show-me variables! Then, I save my workspace with other name (test2.rdata, for example) and close my E session. When I start up R by double-click in my new RData file (test2.rdata) and prompted the command ls(), this show-me: ls() character(0) and I don't see my variables... One information that I don't mentioned: My Rprofile.site have dozen of personal functions, but all *very simple functions*, I don't make change in defaults settings... Cleber ___ Experimente já e veja as novidades. __ 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] double-click in RData file versus load( file )
Please clarify. What happens? On Jan 26, 2008 5:02 PM, Cleber Nogueira Borges [EMAIL PROTECTED] wrote: hi, I tried this approach, but don't work too! (Duncan Murdoch make this suggestion) Cleber OK. The system only knows about one R version. What about the answer to my original second question. If you start up R and then load the .Rdata file (which you previously indicated works) and then save your workspace using a different name from the original Rdata file and then double click on that new Rdata file does that get you the variables in the new Rdata file? ___ Yahoo! Mail - Sempre a melhor opção para você! Experimente já e veja as novidades. http://br.yahoo.com/mailbeta/tudonovo/ __ 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 apply the wilcox_test function to subsets ?
Dupouey Jean-Luc [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]:
On my system wilcox.test() exists, whereas wilcox_test() did not.
Help.search(wilcox_test) does not produce any clues. If you are using
a test from another package, you should specify which package the test
comes from. Web searching produces links to package coin.
Have you tried?
wtest - by(mydata, mydata$myindice, function (x) {
wilcox_test(value~fact, data=x)})
slight modification to the wilcox_test example data--
mydata
pd age grp
1 0.80 At term 1
2 0.83 At term 2
3 1.89 At term 1
4 1.04 At term 2
5 1.45 At term 1
6 1.38 At term 2
7 1.91 At term 1
8 1.64 At term 2
9 0.73 At term 1
10 1.46 At term 2
11 1.15 12-26 Weeks 1
12 0.88 12-26 Weeks 2
13 0.90 12-26 Weeks 1
14 0.74 12-26 Weeks 2
15 1.21 12-26 Weeks 1
16 1.10 12-26 Weeks 2
wilcoxtest - by(mydata, mydata$grp, function(x)
+ {wilcox_test(pd~age, data=x)}
+ )
wilcoxtest
Asymptotic Wilcoxon Mann-Whitney Rank Sum Test
data: pd by age (12-26 Weeks, At term)
Z = -0.4472, p-value = 0.6547
alternative hypothesis: true mu is not equal to 0
---
Asymptotic Wilcoxon Mann-Whitney Rank Sum Test
data: pd by age (12-26 Weeks, At term)
Z = -1.3416, p-value = 0.1797
alternative hypothesis: true mu is not equal to 0
--
David Winsemius
I want to apply a Wilcoxon test on subsets of the data frame mydata,
splitted using the myindice variable. When I send :
wilcoxtest - by(mydata, mydata$myindice, function(x)
{wilcox_test(x$value~x$fact)})
I get :
Error in eval(expr, envir, enclos) : object x not found
whereas
wilcoxtest - by(mydata, mydata$myindice, function(x)
{wilcox.test(x$value~x$fact)})
works !
Why does it fail with the wilcox_test only? And, most important, how
can I apply the wilcox_test function to subsets of mydata splitted
according to mydata$myindice ?
__
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] Error: C stack usage is too close to the limit
Your function has 4 parameters and you are only calling with two. The
first statement:
caldist - function(cage=Cage, error=Error, sdev=Sdev, times=Times, By=By)
{
theta - seq(min(calcurve[,1]), max(calcurve[,1]), by=By);
use By which is not defined.
On Jan 26, 2008 4:29 PM, Maarten Blaauw [EMAIL PROTECTED] wrote:
Lately R has been behaving strange on my Linux (Ubuntu 7.10) machine,
with occasional segfaults. Today something else and reproducible
happened:
If I type the code below (meant for calibrating data), I get the error
message that the C stack usage is too close to the limit.
calcurve - cbind(1:2e4, 1:2e4, 1:2e3); #dummy curve, real one is more complex
caldist - function(cage=Cage, error=Error, sdev=Sdev, times=Times, By=By)
{
theta - seq(min(calcurve[,1]), max(calcurve[,1]), by=By);
interpolate - function(th, col)
{
if(th==calcurve[1,1]) {calcurve[1,col]}else
if(th==calcurve[nrow(calcurve),1]) {calcurve[nrow(calcurve),col]}else
{
k - min(which(calcurve[,1] th));
slope -
(calcurve[k-1,col]-calcurve[k,col])/(calcurve[k-1,1]-calcurve[k,1]);
calcurve[k-1,col] + slope*(th-calcurve[k-1,1]);
}
}
mu - c();
cerror - c();
for(i in 1:length(theta))
{
mu[i] - interpolate(theta[i],2);
cerror[i] - interpolate(theta[i],3);
}
caldist - dnorm(mu, cage, (error^2+cerror^2)^.5);
cbind(theta, caldist/sum(caldist));
}
caldist(1e3,1e2);
Unfortunately I am no huge computer wizard. Has anyone got any idea
why this happens? Is it reproducible on other machines? How can I
solve this problem?
My R:
R version 2.6.1 (2007-11-26)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
Cstack_info()
sizecurrent direction eval_depth
8388608 2404 1 2
Many thanks,
Maarten Blaauw
--
Dr. Maarten Blaauw
School of Geography, Archaeology Palaeoecology
Queen's University Belfast, U.K.
On leave from Department of Earth Sciences
Uppsala University, Sweden
[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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
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Re: [R] double-click in RData file versus load( file )
You could try Rgui --vanilla so that it does not run the scripts you have set up. On Jan 26, 2008 5:31 PM, Cleber Nogueira Borges [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: Please clarify. What happens? ok! I start up the R, load my file by win menu: Load Workspace, ls() show-me variables! Then, I save my workspace with other name (test2.rdata, for example) and close my E session. When I start up R by double-click in my new RData file (test2.rdata) and prompted the command ls(), this show-me: ls() character(0) and I don't see my variables... One information that I don't mentioned: My Rprofile.site have dozen of personal functions, but all *very simple functions*, I don't make change in defaults settings... Cleber __ 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] double-click in RData file versus load( file )
hi Gabor,
I try it:
in *MS-DOS*:
C:\R\etcRgui --vanilla
In *R*:
a=1
b=2
c=3
save.image(c:\\R\\etc\\test.rdata)
q('no')
then I double-clicked' in 'test.rdata' (in c:\R\etc folder)
The R start without my variables: a,b,c
If I make again: R -- vanilla, and then load file, the variables are there!
It is intrigant for me! :-(
Cleber
You could try
Rgui --vanilla
so that it does not run the scripts you have set up.
___
Experimente já e veja as novidades.
__
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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.
[R] REvolution
Does anyone know any more than is in the following press release about REvolution Computing and their commercialization of R? http://www.intel.com/capital/news/releases/080122.htm Intel Capital, the global investment arm of Intel Corporation, today announced that it has invested in the Series A financing of REvolution Computing, creator of parallel computing software for computational statistics R has become the de-facto statistical language and REvolution Computing's R-based solutions provide the necessary scale and support for its growing commercial usage,” said Andre M. Boisvert, Revolution Computing board member. “With this investment, Revolution Computing can deliver the type of performance that has been missing in existing computational statistics offerings. For more information on Revolution Computing, RPro, and ParallelR, visit www.revolution-computing.com At present though, unless you have better success than me, all you will get from the Revolution Computing site is a revolutionary song! John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. __ 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] double-click in RData file versus load( file )
Try entering this at the Windows console:
assoc .Rdata
assuming the answer is:
.Rdata=RWorkspace
try this:
ftype RWorkspace
That will show you what command is executed when you double
click on an Rdata file. Perhaps you need to change that.
On Jan 26, 2008 6:40 PM, Cleber Nogueira Borges [EMAIL PROTECTED] wrote:
hi Gabor,
I try it:
in *MS-DOS*:
C:\R\etcRgui --vanilla
In *R*:
a=1
b=2
c=3
save.image(c:\\R\\etc\\test.rdata)
q('no')
then I double-clicked' in 'test.rdata' (in c:\R\etc folder)
The R start without my variables: a,b,c
If I make again: R -- vanilla, and then load file, the variables are there!
It is intrigant for me! :-(
Cleber
You could try
Rgui --vanilla
so that it does not run the scripts you have set up.
___
Yahoo! Mail - Sempre a melhor opção para você!
Experimente já e veja as novidades.
http://br.yahoo.com/mailbeta/tudonovo/
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Is there a safe mode?
Hi, My R just froze. I can't get it to do anything. It gives Error: band value message to everything I type. Does anyone know if R has a safe mode that I could check for errors and perform diagnostics? I am using R 2.6.1 on Windows XP. ls() Error: bad value search() Error: bad value ?ls Error: bad value q() Error: bad value -- Tom [[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] Error: C stack usage is too close to the limit
Sorry, indeed I forgot to put some of the factors in the code. Here it
is again, now updated:
calcurve - cbind(1:2e4, 1:2e4, rep(100, length=2e4));
caldist - function(cage, error, sdev=2, times=5, By=1)
{
calcurve - calcurve[which((calcurve[,2]+calcurve[,3]) =
cage-(times*error)),];
calcurve - calcurve[which((calcurve[,2]-calcurve[,3]) =
cage+(times*error)),];
theta - seq(min(calcurve[,1]), max(calcurve[,1]), by=By);
interpolate - function(th, col)
{
if(th==calcurve[1,1]) {calcurve[1,col]}else
if(th==calcurve[nrow(calcurve),1]) {calcurve[nrow(calcurve),col]}else
{
k - min(which(calcurve[,1] th));
slope -
(calcurve[k-1,col]-calcurve[k,col])/(calcurve[k-1,1]-calcurve[k,1]);
calcurve[k-1,col] + slope*(th-calcurve[k-1,1]);
}
}
mu - c();
cerror - c();
for(i in 1:length(theta))
{
mu[i] - interpolate(theta[i],2);
cerror[i] - interpolate(theta[i],3);
}
caldist - dnorm(mu, cage, (error^2+cerror^2)^.5);
cbind(theta, caldist/sum(caldist));
}
caldist(2450,50);
Strangely enough the stacking error message seems not to happen every
time. It also has happened on the WinXP partition of the same Toshiba
laptop. So it is not as reproducible as I first hoped/feared.
--
Dr. Maarten Blaauw
School of Geography, Archaeology Palaeoecology
Queen's University Belfast, U.K.
On leave from Department of Earth Sciences
Uppsala University, Sweden
[EMAIL PROTECTED]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparison of aggregate in R and group by in mysql
huali, if i were you, i will create a view on the MySql server to aggregate the data first and then use R to pull the data through this created view. This is not only applicable to R but also a general guideline in similar situation. Per my understanding and experience, R is able to do data manipulation reasonably well. However, we should always use the right tool to do the right thing. On Jan 26, 2008 6:45 PM, zhihuali [EMAIL PROTECTED] wrote: Hi, netters, First of all, thanks a lot for all the prompt replies to my earlier question about merging data frames in R. Actually that's an equivalence to the join clause in mysql. Now I have another question. Suppose I have a data frame X with lots of columns/variables: Name, Age,Group, Type, Salary. I wanna do a subtotal of salaries: aggregate(X$Salary, by=list(X$Group,X$Age,X$Type),Fun=mean) When the levels of Group and Type are huge, it took R forever to finish the aggregation. And I used gc to find that the memory usage was big too. However, in mysql, it took seconds to finish a similar job: select Group,Age,Type ,avg(Salary) from X group by Group,Age,Type Is it because mysql is superior in doing such kind of things? Or my R command is not efficient enough? Why did R have to consume huge memories to do the aggregation? Thanks again! Zhihua Li _ 天凉了，添衣了，心动了，七件了 http://get.live.cn [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === WenSui Liu Statistical Project Manager ChoicePoint Precision Marketing (http://spaces.msn.com/statcompute/blog) === __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparison of aggregate in R and group by in mysql
How does the it compare if you read it into R and then do your aggregate with sqldf: library(sqldf) # example using builtin data set CO2 CO2agg - sqldf(select Plant, Type, Treatment, avg(conc) from CO2 group by Plant, Type, Treatment) # or using your data: Xagg - sqldf(select Group, Age, Type, avg(Salary) from X group by Group, Age, Type) On Jan 26, 2008 6:45 PM, zhihuali [EMAIL PROTECTED] wrote: Hi, netters, First of all, thanks a lot for all the prompt replies to my earlier question about merging data frames in R. Actually that's an equivalence to the join clause in mysql. Now I have another question. Suppose I have a data frame X with lots of columns/variables: Name, Age,Group, Type, Salary. I wanna do a subtotal of salaries: aggregate(X$Salary, by=list(X$Group,X$Age,X$Type),Fun=mean) When the levels of Group and Type are huge, it took R forever to finish the aggregation. And I used gc to find that the memory usage was big too. However, in mysql, it took seconds to finish a similar job: select Group,Age,Type ,avg(Salary) from X group by Group,Age,Type Is it because mysql is superior in doing such kind of things? Or my R command is not efficient enough? Why did R have to consume huge memories to do the aggregation? Thanks again! Zhihua Li _ 天凉了，添衣了，心动了，七件了 http://get.live.cn [[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] Is there a safe mode?
When and how does this happen? In Rgui or Rterm? How do you launch R? Have you tried the obvious and restarted R? If you share the startup messages, sessionInfo() and everything else you think could be helpful, someone might be able to help you. There is a vanilla options to start R, e.g. Rterm --vanilla that you might wanna try. /Henrik On Jan 26, 2008 3:54 PM, tom soyer [EMAIL PROTECTED] wrote: Hi, My R just froze. I can't get it to do anything. It gives Error: band value message to everything I type. Does anyone know if R has a safe mode that I could check for errors and perform diagnostics? I am using R 2.6.1 on Windows XP. ls() Error: bad value search() Error: bad value ?ls Error: bad value q() Error: bad value -- Tom [[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] double-click in RData file versus load( file )
hi Gabor,
Now, seems an light, because...
C:\R\etcassoc .Rdata
.Rdata=RWorkspace
C:\R\etcftype RWorkspace
Tipo de arquivo 'RWorkspace' não encontrado ou nenhum comando open
associado a ele.
*File type 'RWorkspace' not found or none command open associated for it*.
seems something with error here...
but in regedit:
HKEY_CLASSES_ROOT\RWorkspace\shell\open\comand
tipo=REG_SZ
*{{{type}}}*
dados = C:\R\bin\RGui.exe %1 *{{{data}}}*
How to modify a ftype association?
Cleber
Try entering this at the Windows console:
assoc .Rdata
assuming the answer is:
.Rdata=RWorkspace
try this:
ftype RWorkspace
That will show you what command is executed when you double
click on an Rdata file. Perhaps you need to change that.
___
Experimente já e veja as novidades.
__
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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] double-click in RData file versus load( file )
On 26/01/2008 5:31 PM, Cleber Nogueira Borges wrote: Gabor Grothendieck wrote: Please clarify. What happens? ok! I start up the R, load my file by win menu: Load Workspace, ls() show-me variables! Then, I save my workspace with other name (test2.rdata, for example) and close my E session. When I start up R by double-click in my new RData file (test2.rdata) and prompted the command ls(), this show-me: ls() character(0) and I don't see my variables... One information that I don't mentioned: My Rprofile.site have dozen of personal functions, but all *very simple functions*, I don't make change in defaults settings... You might want to temporarily rename that file so that it is not run; I don't think it should interfere, but maybe it does... 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] REvolution
http://www.revolution-computing.com/revolution_company.html seems to lead to something albeit vague. Lots of apparently big names but no indication of what added value the company might bring to an R user. --- John Maindonald [EMAIL PROTECTED] wrote: Does anyone know any more than is in the following press release about REvolution Computing and their commercialization of R? http://www.intel.com/capital/news/releases/080122.htm Intel Capital, the global investment arm of Intel Corporation, today announced that it has invested in the Series A financing of REvolution Computing, creator of parallel computing software for computational statistics R has become the de-facto statistical language and REvolution Computing's R-based solutions provide the necessary scale and support for its growing commercial usage,� said Andre M. Boisvert, Revolution Computing board member. �With this investment, Revolution Computing can deliver the type of performance that has been missing in existing computational statistics offerings. For more information on Revolution Computing, RPro, and ParallelR, visit www.revolution-computing.com At present though, unless you have better success than me, all you will get from the Revolution Computing site is a revolutionary song! John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. __ 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] interactive menu in scripts
On 26/01/2008, WCD [EMAIL PROTECTED] wrote:
Yes, the switch function works fine.
To store generated values in some variable I just use:
switch(menu(c(Normal, Uniform)), a-rnorm(5), a-runif(5))
But why does not work this? (I know there is waste of variables, but in
principle):
b-numeric(10)
switch(menu(c(Normal, Uniform)), a-1, a-2)
if(a==1) {b-rnorm(10)} else {b-runif(10)}
When I run these commands from a script, the choice is offered after the
condition is performed, so b stores ten zeros.
b - switch(menu(c(Normal, Uniform)), rnorm(10), runif(10))
Also readline() function seems to be what I am looking for. But I did not
manage to use it for my reason; this does not work too:
var-numeric(5) #Is not necessary
rdf-function() {
x-readline(Enter 1 for normal, 2 for uniform distribution )
if (x==1) {var-rnorm(5)} else {var-runif(5)}
}
rdf()
You need return the var object in the function
rdf-function() {
x-readline(Enter 1 for normal, 2 for uniform distribution )
if (x==1) {var-rnorm(5)} else {var-runif(5)}
return(var)
}
rdf()
Even this does not work (object x is not found):
rdf2-function() {
x-readline(enter your year of birth )
}
rdf2()
The same that the previous, in this case return(x)
Can you see what am I doing wrong?
Anyway, I am sorry for my maybe bizzar explanations. I am quitr new to R and
R forum.
My aim is to write an R script, where the user can make some choices or set
some parameters via the R console. Filip Kral.
Henrique Dallazuanna wrote:
Try like this:
switch(menu(c(Normal, Poisson)), rnorm(5), rpois(5, 3))
On 25/01/2008, WCD [EMAIL PROTECTED] wrote:
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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--
View this message in context:
http://www.nabble.com/interactive-menu-in-scripts-tp15095049p15111894.html
Sent from the R help mailing list archive at Nabble.com.
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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Re: [R] Comparison of aggregate in R and group by in mysql
How large is your dataframe? How much memory do you have on your system? Are you paging? Here is a test I ran with a data frame with 1,000,000 entries and it seems to be fast: n - 100 x - data.frame(A=sample(LETTERS,n,TRUE), B=sample(letters[1:4],n,TRUE), + C=sample(LETTERS[1:4], n, TRUE), data=runif(n)) system.time(x.agg - aggregate(x$data, list(x$A, x$B, x$C), mean)) user system elapsed 2.650.343.00 On Jan 26, 2008 6:45 PM, zhihuali [EMAIL PROTECTED] wrote: Hi, netters, First of all, thanks a lot for all the prompt replies to my earlier question about merging data frames in R. Actually that's an equivalence to the join clause in mysql. Now I have another question. Suppose I have a data frame X with lots of columns/variables: Name, Age,Group, Type, Salary. I wanna do a subtotal of salaries: aggregate(X$Salary, by=list(X$Group,X$Age,X$Type),Fun=mean) When the levels of Group and Type are huge, it took R forever to finish the aggregation. And I used gc to find that the memory usage was big too. However, in mysql, it took seconds to finish a similar job: select Group,Age,Type ,avg(Salary) from X group by Group,Age,Type Is it because mysql is superior in doing such kind of things? Or my R command is not efficient enough? Why did R have to consume huge memories to do the aggregation? Thanks again! Zhihua Li _ 天凉了，添衣了，心动了，七件了 http://get.live.cn [[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? __ 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] need help opening a file
Sudhindra, You should read the Posting Guide before asking for help: http://www.R-project.org/posting-guide.html It has greats hints on how to solve problems like this yourself, and you should try them before posting. It might suggest that this is a good thing to run in R if you need help with data 'export': RSiteSearch(export) The first hit produced is the manual 'R Data Import/Export', which is provided along with your installation. When you look there you will find this section: 1.2 Export to text files RSiteSearch() also gives hits from this newslist from people like yourself who could not figure out how to export their data. Reading those should help you. HTH, Chuck On Sat, 26 Jan 2008, Sudhindra Gadagkar wrote: Hi, I can't believe I am unable to do this. I just installed R (never used it before, but want to learn it). At present, though. all I want to do is export a data file (specifically crabs in the MASS library) to a text file for use in SPSS. It allows me to peek into the dataset, using the command head(crabs) but I can neither view the entire file nor can I seem to export it to a text file. I have been trying to get help from the online help for several hours now! Maybe I just don't know what to search for. Frustrating! Help would be much appreciated. Thx, S. [[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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ 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] need help opening a file
Sudhindra Gadagkar [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Hi, I can't believe I am unable to do this. I just installed R (never used it before, but want to learn it). At present, though. all I want to do is export a data file (specifically crabs in the MASS library) to a text file for use in SPSS. It allows me to peek into the dataset, using the command head(crabs) but I can neither view the entire file nor can I seem to export it to a text file. I have been trying to get help from the online help for several hours now! Maybe I just don't know what to search for. Frustrating! Help would be much appreciated. Thx, S. [[alternative HTML version deleted]] write.table should provide the basic function. It is designed to write datafames: write.table(crabs, file=crab.out.csv, sep=,) ... will give you a comma separated file: ... first five lines sp,sex,index,FL,RW,CL,CW,BD 1,B,M,1,8.1,6.7,16.1,19,7 2,B,M,2,8.8,7.7,18.1,20.8,7.4 3,B,M,3,9.2,7.8,19,22.4,7.7 4,B,M,4,9.6,7.9,20.1,23.1,8.2 . . . If you are working in Windows, and want to specify a directory, you need to use forward slashes in the full filename. The backslash character has special meaning in *NIX systems, which is where R was developed. If you want to see the dataframe, crabs, just type the name. You should see 200 lines of data. -- 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] need help opening a file
first of all, which is your code to export the data in R? did you use write.table? secondly, it is totally a waste of time to export data from R for use in spss. for whatever can be done by spss, r can handle better. On Jan 26, 2008 9:38 PM, Sudhindra Gadagkar [EMAIL PROTECTED] wrote: Hi, I can't believe I am unable to do this. I just installed R (never used it before, but want to learn it). At present, though. all I want to do is export a data file (specifically crabs in the MASS library) to a text file for use in SPSS. It allows me to peek into the dataset, using the command head(crabs) but I can neither view the entire file nor can I seem to export it to a text file. I have been trying to get help from the online help for several hours now! Maybe I just don't know what to search for. Frustrating! Help would be much appreciated. Thx, S. [[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. -- === WenSui Liu Statistical Project Manager ChoicePoint Precision Marketing (http://spaces.msn.com/statcompute/blog) __ 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] Weighted least squares +AR1 in gls
Hi, I’m using the gls function to fit a model with autoregressive residuals. Does anyone know how to do weighted least squares with autoregressive residuals in gls? Thanks, Sincerely, Xiaopeng __ 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 on R for loops
Hi, all.
I need help on improving the efficiency of my R
simulations. Below is a function that simulates a
change point model. It first generates a sequence of
three dimensional ARMA(1,1) observations, then
calculates the one step ahead prediction errors, some
statistic is calcualted and compared with threshold
values in the end. As you can see in the function,
there are 5 for loops, which makes the simulation long
and inefficient. Can anyone help me improve it?
simfun-function(b){
for(l in 1:20)
{
qq-matrix(0,2,40)
for (w in 1:40)
{
x2 - matrix(rep(0,6000),nr=3)
epsilonzero2-(mvrnorm(n=1,mu=c(0,0,0),Sigma=residsigma))
x2[,1:2]-c(0,0,0)
for (i in 3:550)
{
epsilonone-(mvrnorm(n=1,mu=c(0,0,0),Sigma=residsigma))
x2[,i] -
phi%*%x2[,i-1]+epsilonone-theta%*%epsilonzero2
epsilonzero2-epsilonone
}
residsigma3-matrix(c(0.789,0.2143,0.171,0.2143,1.4394,-0.229,0.171,-0.229,0.6649),nrow=3,byrow=T)
epsilonzero3-epsilonzero2
for (i in 551:2000)
{
epsilonone-(mvrnorm(n=1,mu=c(0,0,0),Sigma=residsigma3))
x2[,i] -
phi%*%x2[,(i-1)]+epsilonone-theta%*%epsilonzero3
epsilonzero3-epsilonone
}
inno2-matrix(0,3,2000)
inno2[,1]-c(0,0,1)
for ( i in 2:2000)
{
inno2[,i]-x2[,i]-phi%*%x2[,(i-1)]+
theta%*%inno2[,(i-1)]
}
sampeigen4-matrix(0,3,(2000-nnumber[l]))
for ( i in (nnumber[l]+1):2000)
{
var1-matrix(0,3,3)
for ( j in 1:(nnumber[l]))
{
var1-var1+j^{b}*inno2[,i-nnumber[l]-1+j]%*%t(inno2[,i-nnumber[l]-1+j])/(sum(c(1:nnumber[l])^{b}))
var1-var1
}
sampeigen4[,(i-nnumber[l])]-(eigen(var1)$values-eigen(residsigma)$values)
}
chisqstat-rep(0,(2000-nnumber[l]))
for(i in 1:(2000-nnumber[l]))
{
chisqstat[i]-((nnumber[l]-1)/2)*t(sampeigen4[,i])%*%(diag(eigen(residsigma)$values)^2)%*%(sampeigen4[,i])
}
normstat-apply((sampeigen4+eigen(residsigma)$values),2,prod)
qq[1,w]-vp(chisqstat[(550-nnumber[l]):(2000-nnumber[l])])
qq[2,w]-vp1(normstat[(550-nnumber[l]):(2000-nnumber[l])])
}
inarl2[,l]-apply(qq,1,mean)
}
inarl2
}
Thanks
XS
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[R] Likelihood optimization numerically
Dear List, I am not sure how should i optimize a log-likelihood numerically: Here is a Text book example from Statistical Inference by George Casella, 2nd Edition Casella and Berger, Roger L. Berger (2002, pp. 355, ex. 7.4 # 7.2.b): data = x = c(20.0, 23.9, 20.9, 23.8, 25.0, 24.0, 21.7, 23.8, 22.8, 23.1, 23.1, 23.5, 23.0, 23.0) n - length(x) # likelihood from a 2 parameter Gamma(alpha, beta), both unknown llk = -n*log(gamma(alpha)) - n*alpha*log(beta) + (alpha - 1)*(sum(log(x))) - (sum(x))/beta # analytic 1st derivative solution w.r.t alpha, assuming beta known # by putting MLE of beta = sum(x)/(n*alpha) # (to simplify as far as possible analytically) llk.1st = - n*digamma(alpha) -n*(log(sum(x)/(n*alpha))+1) + (sum(log(x))) It feels like i should use nls(... , trace=T, start=c(alpha=...),nls.control(maxiter=100,tol=.1)) but not sure how. Can anyone provide me hint? Thank you for your time. Ehsan http://www.youtube.com/profile_play_list?user=wildsc0p R.Version() $platform [1] i386-pc-mingw32 $arch [1] i386 $os [1] mingw32 $system [1] i386, mingw32 $status [1] $major [1] 2 $minor [1] 6.1 $year [1] 2007 $month [1] 11 $day [1] 26 $`svn rev` [1] 43537 $language [1] R $version.string [1] R version 2.6.1 (2007-11-26) Be a better friend, newshound, and __ 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] Likelihood optimization numerically
You asked for a hint. library(MASS) x - c(20.0, 23.9, 20.9, 23.8, 25.0, 24.0, 21.7, 23.8, 22.8, 23.1, 23.1, 23.5, 23.0, 23.0) fitdistr(x, gamma) shape rate 316.56387213.780766 (119.585534) ( 5.209952) To do it with more general and elementary tools, look at ?optim nls(...)? Not relevant at all, no matter how it feels. 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 Mohammad Ehsanul Karim Sent: Sunday, 27 January 2008 4:48 PM To: r-help@r-project.org Subject: [R] Likelihood optimization numerically Dear List, I am not sure how should i optimize a log-likelihood numerically: Here is a Text book example from Statistical Inference by George Casella, 2nd Edition Casella and Berger, Roger L. Berger (2002, pp. 355, ex. 7.4 # 7.2.b): data = x = c(20.0, 23.9, 20.9, 23.8, 25.0, 24.0, 21.7, 23.8, 22.8, 23.1, 23.1, 23.5, 23.0, 23.0) n - length(x) # likelihood from a 2 parameter Gamma(alpha, beta), both unknown llk = -n*log(gamma(alpha)) - n*alpha*log(beta) + (alpha - 1)*(sum(log(x))) - (sum(x))/beta # analytic 1st derivative solution w.r.t alpha, assuming beta known # by putting MLE of beta = sum(x)/(n*alpha) # (to simplify as far as possible analytically) llk.1st = - n*digamma(alpha) -n*(log(sum(x)/(n*alpha))+1) + (sum(log(x))) It feels like i should use nls(... , trace=T, start=c(alpha=...),nls.control(maxiter=100,tol=.1)) but not sure how. Can anyone provide me hint? Thank you for your time. Ehsan http://www.youtube.com/profile_play_list?user=wildsc0p R.Version() $platform [1] i386-pc-mingw32 $arch [1] i386 $os [1] mingw32 $system [1] i386, mingw32 $status [1] $major [1] 2 $minor [1] 6.1 $year [1] 2007 $month [1] 11 $day [1] 26 $`svn rev` [1] 43537 $language [1] R $version.string [1] R version 2.6.1 (2007-11-26) Be a better friend, newshound, and __ 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.
