Query regarding MEMMA output

I had a question regarding MEMMA's output. Reading the documentation I got the impression that I could extract variance components and $\hat{u}$ for each random effect specified, but in my attempt to create a genetic model with two random effects, I only see one random component.

Here is a minimal example where I attempt to perform a single random marker test with background genetic effects.

###R and package version
>packageVersion('sommer')
[1] ‘4.1.3’
> R.version$version.string
[1] "R version 4.0.4 (2021-02-15)"

####Define your design and covariance matrices####
Z1<- apply(as.matrix(dat[,c(11:13)]),2,
             function(x) as.integer(x*2)) #your qtl effects based on 3 founders of population
K1<- diag(ncol(Z1)) #Single variance with no covariance among founder effects
dimnames(K1)<-list(colnames(Z1),colnames(Z1)) 
Z2<-model.matrix(~-1+geno,data=dat) #Your background genetic effects
K2<- Gmat # additive covariance matrix
X<- model.matrix(~1+block,data=dat) #Fixed trial effects
Z<- list(qtl=list(Z=Z1,K=K1),
           poly=list(Z=Z2,K=K2))

testMod<-tryCatch({
   MEMMA(Y=dat$yield
       X=X,ZETA=Z,silent=F)
       },
   error=function(c){
      cat(c$message,file = "log.txt",append = T)
      return(NULL)
})

Examining the variances, I get the following:

> testMod$var.comp$Vu
         T.1
T.1 26.11816

And extracting the realised effects, I get an array the same size as the original dataset.

> nrow(testMod$u.hat)==nrow(dat)
[1] TRUE

I was expecting mod$u.hat to only contain the effects from Z1 and Z2 with the length of the output being the column ranks of Z1 and Z2. I suspect that the output of u.hat is actually the sum of all random effects for each listing in dat.

My question is whether I am mistaken in my understanding of MEMMA or have I made a mistake in how I specified these models?

Thanks in advance.

covaruber / sommer

Query regarding MEMMA output #34