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

Comparative Phylogenetics

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Bootstrapping Likelihood ratios Bootstraps of the likelihood ratio, holding the parameters fixed, finally completed. Anoles: 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: <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. model_bootstrap() bootstraps a single model model_bootstrap_all() applies this to a list of models 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.