lme ->Error in getGroups.data.frame(dataMix, groups)
Didn't read carefully, but: lme does not allow crossed random
effects without considerable effort (there is an example somewhere in
the later chapters of Pinheiro and Bates's book). You r model
specification
test64 <- lme(FinH~SoilNkh + Site + dDDSP + dDDSP2 + Provenance +
Site:Provenance,
random = ~1|Provenance/Genotype + ~1|Site/Block,data=d1)
appears to specify crossed provenance/genotype and site/block REs.
If you can use lme4::lmer it should be easier (note RE is specified as
an additive term within the single formula argument).
On Tue, Dec 11, 2018 at 12:17 PM Boy Possen <bpossen at gmail.com> wrote:
The basic idea is to create a linear model in R such that FinH is explained
by SoilNkh, dDDSP, dDDSP2, Provenance, Site, Genotype and Block, where
SoilNkh, dDDSP and dDDSP2 are continuous covariates, Provenance, Site,
Genotype and Block are factors, Site and Provenance are fixed and Genotype
and Block are random. Also, Genotype is nested within Provenance and Block
within Site.
Since the order the variables go in is of importance, it should be a Anova
type-I with the parameters in following order:
FinH~SoilNkh,Site,dDDSP,dDDSP2,Provenance,Site:Provenance,Provenance/Genotype,Site/Block
For the fixed part I am ok? with either:
test31 <-lm(FinH~SoilNkh + Site + dDDSP + dDDSP2 + Provenance +
Site:Provenance ,data=d1)
test32 <-aov(FinH~SoilNkh + Site + dDDSP + dDDSP2 + Provenance +
Site:Provenance ,data=d1
When trying to specify the random-part, taking the above text as starting
point, trouble starts :)
I feel it should be of the form:
test64 <- lme(FinH~SoilNkh + Site + dDDSP + dDDSP2 + Provenance +
Site:Provenance,
random = ~1|Provenance/Genotype + ~1|Site/Block,data=d1)
but I can't avoid the error
"Error in getGroups.data.frame(dataMix, groups) : invalid formula for
groups"
I am lost for clues, really, so any advice would be great! If any data
should be supplied, I'd be happy to provide of course, but can't (yet)
figure out how...
Thanks in advance for your time.
--
B.J.H.M. Possen
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