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);
|