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emvolz-phylodynamics / phyland

Phylogeographic inference with structured coalescent models
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Add inference of ancestral states #4

Closed sdwfrost closed 7 years ago

sdwfrost commented 7 years ago

To better compare with BEAST output, it would be good to generate estimates of ancestral states at each node in the tree at the ML parameter estimates.

emvolz commented 7 years ago

I added the ace option (default FALSE) If true, it returns a list of interpolating functions for each lineages. Note these are in the order of $bdt$edge.list. These return a vector of probabilities for each deme, eg

f$ace[16] Error in f$ace[16] : Lineage is not extant at given time before most recent sample. Lineage is extant: 0 , 0.346162158894003 time units before most recent sample. f$ace[16] Human Pig 0.4412319 0.5587681