starting values update

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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....