Incorrect XML for up down operator of clock rate and tree for multi-alignment

[walterxie]

BEAUti generates incorrect up down operator of clock rate and tree for multi-alignment

Load multi-alignment, link clock rate but unlink trees, make clock rate be estimated, and then the xml should have up-down for each clock and tree, and a big up-down for all clocks and trees together:

For example, 3 genes:

<operator id="strictClockUpDownOperator.c:Pad_R000255_Scaffold10" scaleFactor="0.9" optimise="false" spec="UpDownOperator" weight="15.0">
    <parameter idref="clockRate.c:Pad_R000255_Scaffold10" name="up"/>
    <tree idref="Tree.t:Pad_R000255_Scaffold10" name="down"/>
</operator>

<operator id="strictClockUpDownOperator.c:Pad_R000272_Scaffold10" scaleFactor="0.9" optimise="false" spec="UpDownOperator" weight="15.0">
    <parameter idref="clockRate.c:Pad_R000255_Scaffold10" name="up"/>
    <tree idref="Tree.t:Pad_R000272_Scaffold10" name="down"/>
</operator>

<operator id="strictClockUpDownOperator.c:Pad_R000333_Scaffold10" scaleFactor="0.9" optimise="false" spec="UpDownOperator" weight="15.0">
    <parameter idref="clockRate.c:Pad_R000255_Scaffold10" name="up"/>
    <tree idref="Tree.t:Pad_R000333_Scaffold10" name="down"/>
</operator>

<operator id="strictClockUpDownOperator.all" scaleFactor="0.95" optimise="false" spec="UpDownOperator" weight="15.0">
    <parameter idref="clockRate.c:Pad_R000255_Scaffold10" name="up"/>
    <tree idref="Tree.t:Pad_R000255_Scaffold10" name="down"/>
    <tree idref="Tree.t:Pad_R000272_Scaffold10" name="down"/>
    <tree idref="Tree.t:Pad_R000333_Scaffold10" name="down"/>
</operator>

[rbouckaert]

The above commits should have fixed the issue, and tests are running fine on my Linux machine, but Hudson does not agree. Still investigating what is going wrong.

[walterxie]

@rbouckaert https://github.com/CompEvol/beast2/commit/733b45177481df913a5554251bd418e31e188857 creates a bug for this issue. When linking clock rate but unlinking tree, the template only creates 1 up-down, because n=1.

<!-- need updown operator for clockRate?!? Also in SubstModel.xml -->
<upDownOperator id='strictClockUpDownOperator.c:$(n)' spec='UpDownOperator' scaleFactor="0.75" weight="3">
   <up idref="clockRate.c:$(n)"/>
   <down idref="Tree.t:$(n)"/>
</upDownOperator>

Is it possible in template to allow the different number of clock rates and trees?

[walterxie]

related to #211

[rbouckaert]

Sharing a clock but not the trees almost certainly implies use of a strict clock model (what other model could be reasonable?). Therefore, a single up-down operator that scales all trees as well as the clock would make sense. Not sure how having multiple up-down operators helps in this situation.

[walterxie]

But the current template is only worked for a single tree, because of $(n) after Tree.t:. When we are talking about all trees, they should be m downs from Tree.t:1 to the last tree Tree.t:m, where n = [1,m].

[alexeid]

Conceptually it would make sense to share the global parameters of a relaxed clock, but obviously not the individual rates on branches which would have to be different for the different trees.

On 14/03/2018, at 3:29 PM, Remco Bouckaert notifications@github.com wrote:

Sharing a clock but not the trees almost certainly implies use of a strict clock model (what other model could be reasonable?). Therefore, a single up-down operator that scales all trees as well as the clock would make sense. Not sure how having multiple up-down operators helps in this situation.

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