Summary:
Variance estimates is a result processing
tool which displays the expected variances of all the independent
parameters of any of the likelihood functions of the most recent
analysis. Covariance Matrix saves the entire covariance
matrix to a file.
Options:
If more than one likelihood function is available, a prompt
will appear, listing all the likelihood functions.
There is also a choice as to which method
to use in computing the Hessian matrix:
- Crude A
faster method which uses 1st order mixed partial derivatives
approximations.
- Finer A
slower method which uses 2nd order mixed partial derivatives
approximations (roughly 4 times slower than Crude).
Output: For
Variance Estimates a table of expected parameter
variances is printed to the console along with the 95% confidence interval.
Example:
VARIANCE ESTIMATES
+-----------------------+---------+------------+--------------------+
| Parameter | Value | Std. Dev. | 95% Conf. Interval |
+-----------------------+---------+------------+--------------------+
| alpha | 0.1957| 0.02472982|( 0.1472, 0.2441) |
+-----------------------+---------+------------+--------------------+
| R | 26.4535| 0.14911572|( 26.1612, 26.7457) |
+-----------------------+---------+------------+--------------------+
| givenTree.Human.a | 0.0089| 0.00251987|( 0.0040, 0.0139) |
+-----------------------+---------+------------+--------------------+
| givenTree.Chimpanzee.a| 0.0112| 0.00274794|( 0.0058, 0.0166) |
+-----------------------+---------+------------+--------------------+
| givenTree.Gorilla.a | 0.0114| 0.00372113|( 0.0041, 0.0187) |
+-----------------------+---------+------------+--------------------+
| givenTree.Orangutan.a | 0.0525| 0.01182611|( 0.0293, 0.0757) |
+-----------------------+---------+------------+--------------------+
| givenTree.Gibbon.a | 0.0809| 0.01566626|( 0.0502, 0.1116) |
+-----------------------+---------+------------+--------------------+
| givenTree.Node5.a | 0.0197| 0.00783575|( 0.0044, 0.0351) |
+-----------------------+---------+------------+--------------------+
| givenTree.Node3.a | 0.0054| 0.00304295|( 0.0000, 0.0114) |
+-----------------------+---------+------------+--------------------+
For Covariance Matrix, the full
covariance matrix is saved to a file.
Example:
Order of parameters:
K tr.1.a tr.2.a tr.Node1.a tr.3.a tr.4.a
{{ 0.0082979996 ,-0.00045364725,-7.3138357e-05,-0.00016120148,-0.00037530438,-0.00014334637}
{-0.00045364725, 0.00049541356,-9.7033462e-05, 5.9047066e-05, 3.8177046e-05,-1.8211741e-05}
{-7.3138357e-05,-9.7033462e-05, 0.00020498417,-6.1730065e-05,-1.0001024e-05, 1.3160608e-05}
{-0.00016120148, 5.9047066e-05,-6.1730065e-05, 0.00048135161,-9.0633357e-05,-3.7905952e-06}
{-0.00037530438, 3.8177046e-05,-1.0001024e-05,-9.0633357e-05, 0.00049922709,-7.0732617e-05}
{-0.00014334637,-1.8211741e-05, 1.3160608e-05,-3.7905952e-06,-7.0732617e-05, 0.00062770996}}
This matrix can be imported into a spreadsheet as a comma separated file.
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