User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/03/23

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Bootstrapping Likelihood ratios

  • Bootstraps of the likelihood ratio, holding the parameters fixed, finally completed.

Anoles: Anoles LR.png

Summary Anoles table: <syntaxhighlight lang="rsplus"> > summary(anoles_boots)

           [,1]        [,2]       [,3]       [,4]        [,5]

[1,] 0.500000000 0.981399498 0.26514573 0.06668672 0.018154938 [2,] 0.009580545 0.500000000 0.15610274 0.04819938 0.011616566 [3,] 0.039233893 0.075349644 0.50000000 0.05699877 0.005443493 [4,] 0.004211230 0.004592917 0.01389950 0.50000000 0.006648916 [5,] 0.173457542 0.198303402 0.38893099 0.33891430 0.500000000 > </syntaxhighlight>

Labrids: Labrid LR.png

<syntaxhighlight lang="rsplus"> > summary(labrid_boots)

         [,1]         [,2]      [,3] [,4]

[1,] 0.5000000 6.036842e-05 0.0000000 0.0 [2,] 0.5424613 5.000000e-01 0.0000000 0.0 [3,] 0.5546890 4.384114e-01 0.5000000 0.0 [4,] 0.4081957 3.488395e-01 0.0295128 0.5 >

</syntaxhighlight>


Note that the location of the red line now just flips sign in the pairwise comparison.


  • Functions for bootstrapping of the likelihood directly also written. Currently running with 1000 replicates.
  1. model_bootstrap() bootstraps a single model
  2. model_bootstrap_all() applies this to a list of models
  3. plot.model_boots() plots the object returned by bootstrapping all models on a single plot axis.
  • Working on a summary function for both LR and likelihood bootstraps.