[R-sig-ME] Mixed Effects Model

[ONKELINX, Thierry]

Dear Stefan,

Your model specification seems to be correct.

Nested random effects are straightforward in lme

lme(HEIGHT~ISO, random =  ~ 1|EX/EX_TP/TP_PLANT, data=z)

Crossed random effects are harder to do. I think it can be done with the pdBlocked function

Best regards,

Thierry


ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx op inbo.be
www.inbo.be

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-----Oorspronkelijk bericht-----
Van: r-sig-mixed-models-bounces op r-project.org [mailto:r-sig-mixed-models-bounces op r-project.org] Namens Stephen Sefick
Verzonden: woensdag 5 juni 2013 23:17
Aan: r-sig-mixed-models op r-project.org
Onderwerp: [R-sig-ME] Mixed Effects Model

Hello all:

This is my first foray into mixed effects modelling and I have a couple of questions.

I have data that I would like to analyize and I believe that a mixed effects model is the proper thing to use:

fixed effects isolate (factor); response plant height

nested factors:
Time Point (TP) nested in Exp
Plant nested in TP

non-nested factor:
Position (leaf position)

I have explicitly nested the TP in Exp by creating an interaction factor TP:Exp=EX_TP and explicitly nested TP in PLANT and Exp with the factor variable Exp:TP:PLANT=TP_PLANT

I have used the code

lmer(HEIGHT~ISO+(1|EX)+(1|EX_TP)+(1|TP_PLANT)+(1|POSITION), data=z)

to fit this model.  I believe this is the correct specification.  Is this correct?

I would also like to be able to fit this in lme (to be used to create a decision tree in package REEM tree).  I would like to use the REEM tree package to investigate metal concentrations in the data predicting isolate incorperating the experimental structure.

Please let me know if any more information is needed to help answer my questions.  Thank you in advance for all of the help.
kindest regards,

--
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
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sas0025 op auburn.edu
http://www.auburn.edu/~sas0025
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