Reputation: 21
I am using a half-sibling pedigree (individuals, Sires, Dams and groups (populations) assigned). When I run the model I received the message “Terms with zero df listed …” and when I ask for the wald test of fixed effect one of my effects is missing. How does assigning a pedigree to my data effect the degrees of freedom available to test my fixed effects? Below is my code. “sacode” and “treatcode” are my fixed effects I’m interested in. When I run the model and produce the Wald tests “sacode” is not included. I am using asreml-R4 in R studio.
Example pedigree:
> ped2[1:10,]
ID Sire Dam
1 1 0 0
2 2 0 0
3 3 0 0
4 4 0 0
5 5 1 1
6 6 1 1
7 7 1 1
8 8 1 1
9 9 1 1
10 10 1 1
> ped2[515:525,]
ID Sire Dam
515 515 4 4
516 516 4 4
517 517 10 148
518 518 11 152
519 519 9 145
520 520 5 133
521 521 10 149
522 522 7 139
523 523 6 138
524 524 11 151
525 525 9 145
Example code:
> m1 <- asreml(Zlg_1 ~
+ 1 + treatcode + sacode + treatcode:sacode + Age + Mated +
+ Block ,
+ random = ~ vm(ID, ped_ai2) + Dam,
+ data = dat)
Model fitted using the gamma parameterization.
ASReml 4.1.0 Mon Feb 22 11:34:24 2021
LogLik Sigma2 DF wall cpu
1 -1816.164 0.442551 2112 11:34:24 0.0
2 -1744.799 0.379880 2112 11:34:24 0.0
3 -1681.384 0.307075 2112 11:34:24 0.0
4 -1649.280 0.235116 2112 11:34:24 0.0
5 -1637.209 0.159875 2112 11:34:24 0.0
6 -1634.396 0.104286 2112 11:34:24 0.0
7 -1633.798 0.070116 2112 11:34:24 0.0
8 -1633.701 0.052888 2112 11:34:24 0.0
9 -1633.693 0.046869 2112 11:34:24 0.0
10 -1633.693 0.046003 2112 11:34:24 0.0
Terms with zero df listed in attribute 'zerodf' of the wald table.
> wald.asreml(m1)
Wald tests for fixed effects.
Response: Zlg_1
Terms added sequentially; adjusted for those above.
Df Sum of Sq Wald statistic Pr(Chisq)
treatcode 1 0.001408 0.0306 0.8611
Age 1 0.053934 1.1729 0.2788
Mated 1 0.019122 0.4159 0.5190
Block 3 0.228305 4.9650 0.1744
treatcode:sacode 1 0.034669 0.7539 0.3852
residual (MS) 0.045983
I have tried adding and removing different variables to see if any particular variable is creating an issue but the zerodf message comes up no matter what combination of variables are in the model.
Upvotes: 2
Views: 106