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Methodology Questions >> How to >> setting constraints http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1237500416 Message started by Rachel on Mar 19th, 2009 at 3:06pm |
Title: setting constraints Post by Rachel on Mar 19th, 2009 at 3:06pm
Hello,
I’ve been taking a closer look at the ins and outs of setting constraints and the output from my test files is not what I expect. I set up things as follows: DataSet myData = ReadDataFile("/Users/rachel/HYPHY/test.seq"); DataSetFilter ElementFilter = CreateFilter(myData, 1, "0-71"); DataSetFilter ReferenceFilter = CreateFilter(myData, 1, "72-11366"); HarvestFrequencies(obsFreqsRef, ReferenceFilter, 1, 1, 1); HarvestFrequencies(obsFreqsEle, ElementFilter, 1, 1, 1); FMatrix = {{*,mu,mu,mu}{mu,*,mu,mu}{mu,mu,*,mu}{mu,mu,mu,*}}; Model FRef = (FMatrix, obsFreqsRef); Tree myTreeRef = (((hg18, panTro2), rheMac2), (mm8, rn4), canFam2); Model FEle = (FMatrix, obsFreqsEle); Tree myTreeEle = (((hg18, panTro2), rheMac2), (mm8, rn4), canFam2); I build and optimize the likelihood function: LikelihoodFunction theLnLik = (ReferenceFilter, myTreeRef, ElementFilter, myTreeEle); Optimize (params, theLnLik); I now apply the constraints. global G=0; ReplicateConstraint(“this1.?.mu:=G*this2.?.mu”, myTreeEle, myTreeRef); Optimize (params, theLnLik); I get (in part) the following output: G=0.57508 myTreeRef.hg18.mu=0.00597841 myTreeEle.hg18.mu=G*myTreeRef.hg18.mu=0.00343806 myTreeEle.Node2.mu=G*myTreeRef.Node2.mu=0.00980094 I then add another constraint: ClearConstraints(myTreeEle.hg18.mu); global S:>1; myTreeEle.hg18.mu := S*G*myTreeRef.hg18.mu; Optimize (params, theLnLik); : I get (in part) the following output: G=0.482008 S=32.4987 myTreeRef.hg18.mu=0.00548192 myTreeEle.hg18.mu=S*G*myTreeRef.hg18.mu=0.0858723 myTreeEle.Node2.mu=G*myTreeRef.Node2.mu=0.00822833 It seems that G and the branch lengths have been re-optimized. I would like to hold G and the branch lengths constant (at the values obtained under the first set of constraints) and only optimize S. Is there a way to do this and am I correct in my assessment of what is going on? Thanks very much in advance for your help. Cheers, Rachel |
Title: Re: setting constraints Post by Sergei on Mar 19th, 2009 at 6:37pm
Dear Rachel,
Can you attach the batch file to the message because some of the characters were lost in copy/paste. Cheers, Sergei |
Title: Re: setting constraints Post by Rachel on Mar 20th, 2009 at 10:13am
Hi Sergei,
Sorry about that. It looks ok on my browser. The batch file is attached to this message. Thanks Rachel http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=testing.bf (1 KB | )
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Title: Re: setting constraints Post by Sergei on Mar 20th, 2009 at 5:11pm
Dear Rachel,
After Code (] ClearConstraints(myTreeEle.hg18.mu); [/code):
Cheers, Sergei |
Title: Re: setting constraints Post by Rachel on Mar 20th, 2009 at 5:36pm
That answers my question. Thanks very much!
Rachel |
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