Need some help interpreting the summary() -function results.
I am running a
lme from the package
nlme in R.
I have a simple (and quite small) dataset with three grouping variables: origin, genotype and time, response is a continuous variable named Maxi.
Origin = 2 levels, called Ka and La
Genotype = 3 levels nested within origin Ka and 2 levels nested within origin La
Time = 2 levels nested within each genotype
I am interested in the main effects of Origin, Time and their interaction. In addition to testing I'd like to have their estimates. I want to model the random part as Genotype nested within Origin. Here's the model I had in mind:
model = lme(fixed = Maxi ~ Origin*Time, random = ~ 1 |Genotype)
anova()s etc work fine and there's actually no significant interaction, but
here's the problem:
when I run summary(model), I get:
Fixed effects: Maxi ~ Origin * Time Value Std.Error DF t-value p-value (Intercept) 15.399386 1.1127382 20 13.839181 0.0000 OriginLa -1.986388 1.7702416 3 -1.122100 0.3435 Timeeve 0.074444 0.8942694 20 0.083246 0.9345 OriginLa:Timeeve -1.387448 1.5648876 20 -0.886612 0.3858
Where are my estimates for the other levels of the factors? I thought that to be able to interpret these fixed effects the summary-table would have to show all the levels in some manner? Or do I interpret this such that:
- the estimate for OriginKa is 15.399386
- the estimate for OriginLa is 15.399386-1.986388
- the estimate for Timemor is 15.399386
the estimate for Timeeve is 15.399386+0.074444
and then I can't even guess how to interpret the interaction estimate...
It doesn't feel intuitively right that the estimates would be the same for both a level of the Origin -factor and a level of the Time factor.
- I did NOT make my data into a groupedData (is it always necessary?)
- I wanted to include random = 1 ~ |Origin/Genotype in the model but that produced NaNs in the output, apparently the model became too complex or my data is arranged wrongly?
So the Questions are:
- How do I interpret the summary to get the estimates, or is there something wrong here, or is there another way of getting the estimates. I need the estimates for both levels of Time within both Origins.
- How do I specify the random effects with this data structure? Have I done it right?
Here's the data needed to reproduce my problem:
Orig.Genot.Time Maxi Ka Ka1 mor 14,59 Ka Ka1 eve 13,42 Ka Ka11 mor 14,08 Ka Ka11 eve 16,29 Ka Ka15 mor 14,38 Ka Ka15 eve 14,56 La La1 mor 17,82 La La1 eve 13,28 Ka Ka1 mor 16,44 Ka Ka1 eve 15,52 Ka Ka15 mor 13,76 Ka Ka15 eve 13,55 Ka Ka1 mor 19,15 Ka Ka1 eve 19,12 La La6 mor 10,54 La La6 mor 11,38 La La6 eve 10,48 Ka Ka15 mor 15,25 Ka Ka15 eve 16,51 La La1 mor 17,46 La La1 eve 15,57 Ka Ka1 mor 16,83 Ka Ka1 eve 15,63 Ka Ka15 mor 14,54 Ka Ka15 eve 15,09 La La1 mor 11,3 La La1 eve 11,94