Re: [R] Mixed effect model in R

[Lina Jansen]

Thanks for the helping links. Now, I worked out that I have to use the lme4
package (with the lmer function) for my analysis. But now I do not
understand the input to the lmer function.

In the lme function (of the nlme package) the correct input would in my case
be:

lme(fixed=Ac_LC~cond_ind,random=~img_cond|sub_ind/cond_ind)

but also after reading the help and the R news I do not understand the
formula I have to use for the lmer function. Could someone help me
translating the lme input to a lmer input? And does someone know of a good
explanation of the kinds of formulas you can input? In the books they only
explain the lme input.

Thanks,
Lina

2006/10/17, Stefan Grosse [EMAIL PROTECTED]:

 Please always reply to the list as well as there always might be someone
 faster/better answering (or it could be that I am wrong, so someone
 might correct me)

 Indeed Pinheiro/Bates assume gaussian error terms... but I am not really
 sure whether you meant that with  non normally distributed respond
 variable resp. with non-normal data

 however:
 / Mixed-effects models: / The recommended nlme
 http://cran.r-project.org/src/contrib/Descriptions/nlme.html package,
 associated with Pinheiro and Bates, / Mixed-Effects Models in S and
 S-PLUS / (Springer, 2000), fits linear and nonlinear mixed-effects
 models, commonly used in the social sciences for hierarchical and
 longitudinal data. Generalized linear mixed-effects models may be fit by
 the glmmPQL function in the MASS package, and by the lmer function in
 the Matrix
 http://cran.r-project.org/src/contrib/Descriptions/Matrix.html package
 (related to the lme4
 http://cran.r-project.org/src/contrib/Descriptions/lme4.html package,
 which largely supersedes nlme
 http://cran.r-project.org/src/contrib/Descriptions/nlme.html for /
 linear / mixed models). Also see the lmeSplines
 http://cran.r-project.org/src/contrib/Descriptions/lmeSplines.html and
 lmm http://cran.r-project.org/src/contrib/Descriptions/lmm.html
 packages. [
 http://cran.r-project.org/src/contrib/Views/SocialSciences.html ]

 Lina Jansen schrieb:
 
 
  2006/10/17, Stefan Grosse [EMAIL PROTECTED]
  mailto:[EMAIL PROTECTED]:
 
  Interesting packages for you might be the nlme and lme4 packages
  and as
  a book Pinheiro/Bates, Mixed-Effects Models in S and S-Plus
 
 
  Thank you for the answer. I am always unsure concerning the
  non-normality. Can I use the nlme and lme4 with non-normal data?
  First, I thought they would work like an ANOVA but with random and
  fixed effects.



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[R] Mixed effect model in R

[Lina Jansen]

Hi,

I am analysing an experiment that has one fixed (6 conditions) and two
random factors (11 subjects, 24 images in the conditions). I read somewhere
else that you can also see such a design as a nested experiment with the
hierarchy: subjects - condition - image. For some analysis I have one
respond variable and for others I have more. The response variables are
non-normally distributed. Now the question:

Is there a package that can deal with such a design? I would like to use a
generalized linear model. Are there glms that are extended to do
multivariate analysis (for the 2 random + 1 fixed variable design)? And how
do you call such a design?

Last question: Can you suggest me some literature about such a problem? I am
quite unsure concerning the analysis.

Thanks for any advice
lisra

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[R] Windows/MAC difference (console)

[Lina Jansen]

Hello,

a colleague of mine uses R on his Mac and he has quite a nice feature: When
he starts writing a  part of the function like plot( the programming is
showing him at the bottom the kind of arguments you can input to the
function. He told me that he has not installed any further stuff than the
base R program.

Is this a feature you only have in the MAC version? I really like it. I
tried some editors, but there were all not the thing I would like to
have. I am only searching for such a display and perhaps syntax
highlighting in the console. But I do not want to have all this GUI
stuff like you have in R commander.
Do you have any suggestion?

Thanks in advance,
lisra

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