starting values update
Nadine Mugusa wrote:
Hi all, does anyone know how to automatically update starting values in R?
See ?set.seed Uwe Ligges
I' m fitting multiple nonlinear models and would like to know how I can update starting values without having to type them in. thank all --- On Fri, 12/26/08, r-help-request at r-project.org <r-help-request at r-project.org> wrote: From: r-help-request at r-project.org <r-help-request at r-project.org> Subject: R-help Digest, Vol 70, Issue 26 To: r-help at r-project.org Date: Friday, December 26, 2008, 6:00 AM Send R-help mailing list submissions to r-help at r-project.org To subscribe or unsubscribe via the World Wide Web, visit
https://stat.ethz.ch/mailman/listinfo/r-help or, via email, send a message with subject or body 'help' to r-help-request at r-project.org You can reach the person managing the list at r-help-owner at r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-help digest..." Today's Topics: 1. Re: Implementing a linear restriction in lm() (Ravi Varadhan) 2. p(H0|data) for lm/lmer-objects R (Leo G?rtler) 3. Re: beginner data.frame question (Oliver Bandel) 4. Re: 4 questions regarding hypothesis testing, survey package, ts on samples, plotting (Thomas Lumley) 5. Re: How can I avoid nested 'for' loops or quicken the process? (Oliver Bandel) 6. Re: 4 questions regarding hypothesis testing, survey package, ts on samples, plotting (Peter Dalgaard) 7. Re: 4 questions regarding hypothesis testing, survey package, ts on samples, plotting (Ben Bolker) 8. Re: Class and object problem (Ben Bolker) 9. Re: 4 questions regarding hypothesis testing, survey package, ts on samples, plotting (Peter Dalgaard) 10. Re: p(H0|data) for lm/lmer-objects R (Daniel Malter) 11. Re: Implementing a linear restriction in lm() (Daniel Malter) 12. Re: p(H0|data) for lm/lmer-objects R (Andrew Robinson) 13. Percent damage distribution (diegol) 14. Re: ggplot2 Xlim (Wayne F) 15. Re: creating standard curves for ELISA analysis (1Rnwb) 16. Re: Percent damage distribution (Ben Bolker) 17. Re: How can I avoid nested 'for' loops or quicken the process? (Prof Brian Ripley) 18. Re: Percent damage distribution (Prof Brian Ripley) 19. Upgrading R causes Tinn-R to freeze. (rkevinburton at charter.net) ---------------------------------------------------------------------- Message: 1 Date: Thu, 25 Dec 2008 11:39:33 -0500 From: Ravi Varadhan <rvaradhan at jhmi.edu> Subject: Re: [R] Implementing a linear restriction in lm() To: Serguei Kaniovski <Serguei.Kaniovski at wifo.ac.at> Cc: r-help at stat.math.ethz.ch Message-ID: <f5bef5b03d6.495370f5 at johnshopkins.edu> Content-Type: text/plain; charset=iso-8859-1 Hi, You could use the "offset" argument in lm(). Here is an example: set.seed(123) x <- runif(50) beta <- 1 y <- 2 + beta*x + rnorm(50) model1 <- lm (y ~ x) model2 <- lm (y ~ 1, offset=x) anova(model2, model1) Best, Ravi. ____________________________________________________________________ Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvaradhan at jhmi.edu ----- Original Message ----- From: Serguei Kaniovski <Serguei.Kaniovski at wifo.ac.at> Date: Wednesday, December 24, 2008 9:39 pm Subject: [R] Implementing a linear restriction in lm() To: r-help at stat.math.ethz.ch Dear All! I want to test a coeffcient restriction beta=1 in a univariate model lm (y~x). Entering lm((y-x)~1) does not help since anova test requires the same dependent variable. What is the right way to proceed? Thank you for your help and marry xmas, Serguei Kaniovski ________________________________________ Austrian?Institute?of?Economic?Research?(WIFO) P.O.Box?91??????????????????????????Tel.:?+43-1-7982601-231 1103?Vienna,?Austria????????Fax:?+43-1-7989386 Mail:?Serguei.Kaniovski at wifo.ac.at [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. ------------------------------ Message: 2 Date: Thu, 25 Dec 2008 19:51:36 +0100 From: Leo G?rtler <leog at anicca-vijja.de> Subject: [R] p(H0|data) for lm/lmer-objects R To: r-help at stat.math.ethz.ch Message-ID: <4953D638.4090507 at anicca-vijja.de> Content-Type: text/plain; charset=ISO-8859-15 Dear R-List, I am interested in the Bayesian view on parameter estimation for multilevel models and ordinary regression models. AFAIU traditional frequentist p-values they give information about p(data_or_extreme|H0). AFAIU it further, p-values in the Fisherian sense are also no alpha/type I errors and therefor give no information about future replications. However, p(data_or_extreme|H0) is not really interesting for social science research questions (psychology). Much more interesting is p(H0|data). Is there a way or formula to calculate these probabilities of the H0 (or another hypothesis) from lm-/lmer objects in R? Yes I know that multi-level modeling as well as regression can be done in a purely Bayesian way. However, I am not capable of Bayesian statistics, therefor I ask that question. I am starting to learn it a little bit. The frequentist literature - of course - does not cover that topic. Thanks a lot, best, leo g?rtler ------------------------------ Message: 3 Date: Thu, 25 Dec 2008 19:49:58 +0000 (UTC) From: Oliver Bandel <oliver at first.in-berlin.de> Subject: Re: [R] beginner data.frame question To: r-help at stat.math.ethz.ch Message-ID: <loom.20081225T193443-238 at post.gmane.org> Content-Type: text/plain; charset=us-ascii John Fox <jfox <at> mcmaster.ca> writes: Dear Kirk, Actually, co2 isn't a data frame but rather a "ts" (timeseries) object. A nice thing about R is that you can query and examine objects: class(co2) [1] "ts" [...] Yes. And with frequency(co2) [1] 12 One gets "the number of observations per unit of time". When one sets the parameter "start" and "frequency" or "start" and "deltat" or "start" and "end" of a time-series, one can set the used values and that means that functions that use those values, also will be controlled by this. start(co2) [1] 1959 1 end(co2) [1] 1997 12 Rearranging by creaating a new ts-object with different timely parameters: new_co2 <- ( ts( co2,frequency=1, start=1959) ) start(new_co2) [1] 1959 1 end(new_co2) [1] 2426 1 .... and the way back: old_co2 <- ( ts( new_co2, frequency=12, start=1959) ) start(old_co2) [1] 1959 1 end(old_co2) [1] 1997 12 using plot on those values will result in different plots. Why the mentioned test data is showed different wih summary, [[elided Yahoo spam]] To have the test-data (or the way how it was constructed) could help in helping. Ciao, Oliver ------------------------------ Message: 4 Date: Thu, 25 Dec 2008 12:00:21 -0800 (PST) From: Thomas Lumley <tlumley at u.washington.edu> Subject: Re: [R] 4 questions regarding hypothesis testing, survey package, ts on samples, plotting To: Peter Dalgaard <p.dalgaard at biostat.ku.dk> Cc: r-help at r-project.org, Ben Bolker <bolker at ufl.edu> Message-ID: <Pine.LNX.4.43.0812251200210.24756 at hymn11.u.washington.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed On Wed, 24 Dec 2008, Peter Dalgaard wrote: Ben Bolker wrote: Khawaja, Aman wrote: I need to answer one of the question in my open source test is: What are the four questions asked about the parameters in hypothesis testing? Please check the posting guide. * We don't answer homework questions ("open source" doesn't mean that other people answer the questions for you, it means you can find the answers outside your own head -- and in any case, we don't have any of way of knowing that the test is really open). * this is not an R question but a statistics question * please don't post the same question multiple times Besides, this is really unanswerable without access to your teaching material, which probably has a list of four questions somewhere... Starting with 'Why is this parameter different from all other parameters?', perhaps. It is a bit like the History question: "Who was what in what of whom?" A traditional British equivalent is "Who dragged whom how many times around the walls of where?", which does have just about enough context. The R answer to the original post would probably be 1. Why aren't there any p-values in lmer()? 2. How do I extract p-values from lm()? 3. Can R do post-hoc tests? 4. Can R do tests of normality? and in statistical consulting the questions might be 1. Doesn't that assume a Normal distribution? 2. Do you have a reference for that? 3. What was the power for that test? 4. Can you redo the test just in the left-handed avocado farmers[*] -thomas [*] this particular subset (c) joel on software. Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle ------------------------------ Message: 5 Date: Thu, 25 Dec 2008 20:20:48 +0000 (UTC) From: Oliver Bandel <oliver at first.in-berlin.de> Subject: Re: [R] How can I avoid nested 'for' loops or quicken the process? To: r-help at stat.math.ethz.ch Message-ID: <loom.20081225T201648-168 at post.gmane.org> Content-Type: text/plain; charset=us-ascii Bert Gunter <gunter.berton <at> gene.com> writes: FWIW: Good advice below! -- after all, the first rule of optimizing code is: Don't! For the record (yet again), the apply() family of functions (and their packaged derivatives, of course) are "merely" vary carefully written for() loops: their main advantage is in code readability, not in efficiency gains, which may well be small or nonexistent. True efficiency gains require "vectorization", which essentially moves the for() loops from interpreted code to (underlying) C code (on the underlying data structures): e.g. compare rowMeans() [vectorized] with ave() or apply(..,1,mean). [...] The apply-functions do bring speed-advantages. This is not only what I read about it, I have used the apply-functions and really got results faster. The reason is simple: an apply-function does make in C, what otherwise would be done on the level of R with for-loops. Ciao, Oliver ------------------------------ Message: 6 Date: Thu, 25 Dec 2008 21:25:58 +0100 From: Peter Dalgaard <p.dalgaard at biostat.ku.dk> Subject: Re: [R] 4 questions regarding hypothesis testing, survey package, ts on samples, plotting To: Thomas Lumley <tlumley at u.washington.edu> Cc: r-help at r-project.org, Ben Bolker <bolker at ufl.edu> Message-ID: <4953EC56.9010808 at biostat.ku.dk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Thomas Lumley wrote: On Wed, 24 Dec 2008, Peter Dalgaard wrote: It is a bit like the History question: "Who was what in what of whom?" A traditional British equivalent is "Who dragged whom how many times around the walls of where?", which does have just about enough context. Yes. "Joshua, Isrelites, seven, Jericho" is wrong by a hair....