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  HyPhy Documentation: Miscellaneous: Likelihood Function Output Formats

     HYPHY offers several built in methods of displaying likelihood functions and parameter values. There is an option in the Preferences which allows the user to select which output format will be used by default. Batch language files may override that preference though, by setting the value of LIKELIHOOD_FUNCTION_OUTPUT.

     Standard Tree. This is the default. Likelihood function value is displayed, followed by the list of shared parameters and then by the tree string(s) in Newick format, with branch lengths representing the expected number of substitutions along that branch per unit of evolution (nucleotide, amino acid, codon etc.). Option "Tree with branch lengths" in Preferences:Likelihood Display.


Example:

Log Likelihood = -2617.4840043544;
Shared Parameters:
RelRate=1.159128
R=2.103818
Tree tr2=((1:0.0831293,2:0.132816)Node2:0.0753369,3:0.507847,4:0.42545);
Tree tr1=((1:0.0718295,2:0.114763)Node2:0.0650964,3:0.438815,4:0.367618);

   List. Likelihood function value is displayed, followed by the list of all model parameters. This format can be helpful for tabulating parameter estimates. Option "Complete report as list" in Preferences:Likelihood Display.


Example:

Likelihood Function's Current Value = -2617.4840043544
RelRate=1.159128
R=2.103818
tr1.1.a=0.069970
tr1.2.a=0.111792
tr1.Node2.a=0.063411
tr1.3.a=0.427456
tr1.4.a=0.358102
tr2.1.a=RelRate*tr1.1.a=0.081104
tr2.2.a=RelRate*tr1.2.a=0.129581
tr2.Node2.a=RelRate*tr1.Node2.a=0.073502
tr2.3.a=RelRate*tr1.3.a=0.495476
tr2.4.a=RelRate*tr1.4.a=0.415086

   Parameter List. Produces a list of parameter names and contstraints. Can be useful when designing custom analyses to check correctness of setup. Option "Parameters and Constraints" in Preferences:Likelihood Display.

Example:

Independent Parameters List

Parameter 1 is RelRate
Parameter 2 is R
Parameter 3 is tr1.1.a
Parameter 4 is tr1.2.a
Parameter 5 is tr1.Node2.a
Parameter 6 is tr1.3.a
Parameter 7 is tr1.4.a

Constrained Parameters List

Parameter 1 is tr2.1.a=RelRate*tr1.1.a
Parameter 2 is tr2.2.a=RelRate*tr1.2.a
Parameter 3 is tr2.Node2.a=RelRate*tr1.Node2.a
Parameter 4 is tr2.3.a=RelRate*tr1.3.a
Parameter 5 is tr2.4.a=RelRate*tr1.4.a

   Value Only. Just the likelihood value. Can be of use when tabulating the values of the likelihood function (say for plotting). Option "Function Value Only" in Preferences:Likelihood Display.

Example:

-2617.4840043544

   Batch Language Statement Prodcues a list of parameters, values and constraints as a batch language statement. Can be of use when saving parameter estimates for later use. Option "Batch Language Statement" in Preferences:Likelihood Display.

Example:

global R=9.292513166908901;
givenTree.Human.a=0.01560777149915235;
givenTree.Chimpanzee.a=0.02029540621386441;
givenTree.Gorilla.a=0.02172147255256684;
givenTree.Orangutan.a=0.03778399104333652;
givenTree.Gibbon.a=0.05246268806658547;
givenTree.Node6.a=0.02002671592954166;
givenTree.Node4.a=0.006598763660133528;

   Batch Language Statement with Trees Generates a list of parameters, values, constraints and tree declarations as a batch language statement. Can be of use when saving parameter estimates and tree topologies for later use. Option "Batch Language Statement with Trees" in Preferences:Likelihood Display.

Example:

global R=9.292513166908901;
givenTree.Human.a=0.01560777149915235;
givenTree.Chimpanzee.a=0.02029540621386441;
givenTree.Gorilla.a=0.02172147255256684;
givenTree.Orangutan.a=0.03778399104333652;
givenTree.Gibbon.a=0.05246268806658547;
givenTree.Node6.a=0.02002671592954166;
givenTree.Node4.a=0.006598763660133528;
Tree givenTree=(Human:0.0413358,Chimpanzee:0.0537506, (Gorilla:0.0575275, (Orangutan:0.100068,Gibbon:0.138943)Node6:0.053039)Node4:0.0174763);

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002