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  ASReml  ~  Different variance components, BVs between versions 3 and 4

tshalev
Posted: Wed Dec 05, 2018 10:46 pm Reply with quote
Joined: 03 Mar 2017 Posts: 5
Hi,

I am trying out ASREML version 4, and I have noticed that I am getting different outcomes when compared to version 3. For example, I run this model in 3:

Code:
asreml(data = wrc.pheno.dat,
                          fixed = fath ~ site,
                          random = ~ site:REP + idh(site):REP:SET + ped(tree),
                          rcov = ~ at(site):id(units),
                          ginverse = list(tree = wrc.ainv),
                          na.method.X = "include", na.method.Y = "include",
                          maxit = 100)


And this one in 4:
Code:
asreml(data = wrc.pheno.dat,
                          fixed = fath ~ site,
                          random = ~ site:REP + idh(site):REP:SET + vm(tree, wrc.ainv),
                          residual = ~ dsum(~ id(units) | site),
                          na.action = na.method("include", "include"),
                          maxit = 100)


And I am assuming that these are identical models, although I am not 100% sure. The variance components for the first model (version 3):
Code:
                         gamma  component std.error   z.ratio constraint
site:REP!site.var    3515034.3  3515034.3   1116827  3.147340   Positive
site:REP:SET!site.1  7443651.3  7443651.3   2504858  2.971686   Positive
site:REP:SET!site.2   512916.7   512916.7   2367086  0.216687   Positive
site:REP:SET!site.3 10556786.5 10556786.5   2914884  3.621683   Positive
ped(tree)!ped       13674032.7 13674032.7   3596819  3.801702   Positive
site_1!variance     28316151.5 28316151.5   3338351  8.482077   Positive
site_2!variance     43404937.7 43404937.7   4282322 10.135842   Positive
site_3!variance     26182652.5 26182652.5   3353438  7.807703   Positive


And for the second model (version 4):
Code:
               effect  component std.error   z.ratio bound X.ch vc.percent
1            site:REP  3515194.1   1117124  3.146646     P  0.0  2.6310123
2 site:REP:SET!site_1  7443850.5   2505343  2.971190     P  0.0  5.5714881
3 site:REP:SET!site_2   513183.2   2367278  0.216782     P  0.4  0.3841015
4 site:REP:SET!site_3 10556567.6   2914490  3.622098     P  0.0  7.9012591
5  vm(tree, wrc.ainv) 13673759.4   3596494  3.801970     P  0.0 10.2343792
6            site_1!R 28316194.0   3338246  8.482357     P  0.0 21.1937813
7            site_2!R 43404687.9   4281854 10.136892     P  0.0 32.4870447
8            site_3!R 26182707.7   3353337  7.807955     P  0.0 19.5969338

Not sure why these are different? The breeding values are also different, although they are very strongly correlated (99%).
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