The ASREML list is still not getting through to me.
There is an addressing problem we still have not sorted.
Your .pin file problem is a bug which will occur if you have only
1 or 2 fixed effects in the model. I've now fixed it in my code
which should be available on the website later in the week.
The problem is that it thinks there is an extra set of solutions in the
DENSE equations but they are not there and so the values are zeros.
There is no work around until I fix it.
Note that ASREML does not give the correct SE's for predicted values
when some of the effects are in the SPARSE part of the model.
You need then to specify !DENSE to put them in the !DENSE part
but that only works for some random effects and also seems to be broken at the
> We (Dadan Kusnandar and myself) are trying to get means for levels of a
> random term using a .pin file to combine the parameter estimates in the .sln
> file. The means given are correct except for the first level of the random
> factor, which is being taken to have an effect of zero, and hence is giving
> the grand mean. This is despite the fact that the .sln file does NOT give
> the effect of this level as zero.
> As you will see from our .pin file (appended), we have tried various >
> of specifying the effects we are after - shorthand, longhand, and the
> effects of each level rather than the means. In every case we get the
> result we expect except for Level 1.
> I also append the .pvs file and the first few lines of the .sln file.
> What's going on?
> The examples in the manual that we're following are for the means of
> of a fixed-effect factor, and we suspect that this is related to the
> Best wishes,
> Nick Galwey
# Obtain provenance means
# Provmeans 1 [2:9]
Provmean1 1 2
Provmean2 1 3
Provmean3 1 4
Provmean4 1 5
Provmean5 1 6
Provmean6 1 7
Provmean7 1 8
Provmean8 1 9
'Grandmean ' 1.00000 0.03076 0.15650
'Effect1 ' 1.00000 0.00000 0.00000
'Effect2 ' 1.00000 0.35460 0.78177
'Provmean1 ' 1.00000 0.03076 0.15650
'Provmean2 ' 1.00000 0.38536 0.79728
'Provmean3 ' 1.00000 -0.34114 0.76116
'Provmean4 ' 1.00000 0.17046 0.75600
'Provmean5 ' 1.00000 0.23476 0.79814
'Provmean6 ' 1.00000 -0.58524 0.76202
'Provmean7 ' 1.00000 -0.39054 0.75987
'Provmean8 ' 1.00000 0.47146 0.75558
.sln file (first few lines)
mu 1 0.3076E-01 0.1565
prov 1 0.2701 0.1704
prov 2 0.3546 0.1781
prov 3 -0.3719 0.1697
prov 4 0.1397 0.1685
prov 5 0.2040 0.1783
prov 6 -0.6160 0.1699
prov 7 -0.4213 0.1694
prov 8 0.4407 0.1684
rep 1 -0.2503E-01 0.4021E-01
rep 2 0.1654E-01 0.4053E-01
rep 3 0.8483E-02 0.4036E-01
rep.block 1.0001 -0.9539E-01 0.8190E-01
rep.block 1.0002 -0.1372E-01 0.8434E-01
rep.block 1.0003 0.1655E-01 0.8210E-01
Arthur Gilmour PhD mailto:Arthur.Gilmour@agric.nsw.gov.au
Senior Research Scientist (Biometrics) fax: <61> 2 6391 3899
NSW Agriculture <61> 2 6391 3922
Orange Agricultural Institute telephone work: <61> 2 6391 3815
Forest Rd, ORANGE, 2800, AUSTRALIA home: <61> 2 6362 0046
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