R help - Jul 2007 - The 'REP' term in AMMI{agricolae}

Dear all,

W2k, R 2.5.1

I am trying out the AMMI function in the agricolae package, to analyse the
dependence of environment for a certain cultivar. The function responds to
four basic variables:

ENV Environment
GEN Genotype
REP Replication
Y Response

My question concerns the 'REP' term. When I normally do an analysis of
variance, the replication would refer to repeated observations within the
each field trial. In the case I am analysing right now, I have five years
of observations for each 'ENV', in such a case it feels natural to use
year as the most important replication of the environment- especially as I
am interested in long term trends. This approach also seems to work
allright.

But the field trials are also structured in three main blocks, subdivided
into five 'lattice' blocks, a structure that is powerful in the analysis
of variance. (I use a random call in lme{nlme}).

Is it possible to use the block structure also in the AMMI analysis? If
that is possible, how should I code? I have tried to find out in the
documentation, but if it is stated there I do not understand it.

Thank you
/CG

-- 
CG Pettersson, PhD
Swedish University of Agricultural Sciences (SLU)
Dept. of Crop Production Ecology. Box 7043.
SE-750 07 Uppsala, Sweden
cg.pettersson at vpe.slu.se

The AMMI senso strictu part starts from the corrected data for genotype and
environment. In most cases where AMMI is applied (maybe also in the
agricolae package, I haven't checked), starts from the interaction effects
obtained through a general linear model anova.
It should be possible to replace the input by blups from your mixed model.
R news 7/1 (p14-19) gave some basic code for AMMI. There you should be able
to get ideas how to modify the code.


Joris








                                                                           
             "CG Pettersson"
             <cg.pettersson at vp
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                                       [R] The 'REP' term in
             23/07/2007 19:59          AMMI{agricolae}                     
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Dear all,

W2k, R 2.5.1

I am trying out the AMMI function in the agricolae package, to analyse the
dependence of environment for a certain cultivar. The function responds to
four basic variables:

ENV Environment
GEN Genotype
REP Replication
Y Response

My question concerns the 'REP' term. When I normally do an analysis of
variance, the replication would refer to repeated observations within the
each field trial. In the case I am analysing right now, I have five years
of observations for each 'ENV', in such a case it feels natural to use
year as the most important replication of the environment- especially as I
am interested in long term trends. This approach also seems to work
allright.

But the field trials are also structured in three main blocks, subdivided
into five 'lattice' blocks, a structure that is powerful in the analysis
of variance. (I use a random call in lme{nlme}).

Is it possible to use the block structure also in the AMMI analysis? If
that is possible, how should I code? I have tried to find out in the
documentation, but if it is stated there I do not understand it.

Thank you
/CG

--
CG Pettersson, PhD
Swedish University of Agricultural Sciences (SLU)
Dept. of Crop Production Ecology. Box 7043.
SE-750 07 Uppsala, Sweden
cg.pettersson at vpe.slu.se

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