Area allowed txt file format

[Ned Liu]

Hi everyone,

I hope this post finds you all well. I am trying to construct an area_allowed.txt for my phylogeny. However, unlike the example file, my max_range size=3. I was wondering how I should construct my area_allowed.txt file?

Hawaii example file format (non-stratified; max_range size=2)

K O M H 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

[Ned Liu]

[Nick Matzke]

Hi! areas_allowed is useful for very simple scenarios like islands disappearing back in time, but otherwise, it is safer to use a manual_states_list:

Manually modifying the list of states/ranges — A BETTER SOLUTION than the areas-adjacency matrix

http://phylo.wikidot.com/biogeobears#better_than_adjacency

Except for the simplest cases, manual modification of the states list will work better/be more flexible than attempting to use the areas_adjacency matrix strategy. These links explain how to do it:

Manual modification of states_list (list of geographic ranges, a.k.a. the list of states in the state space)
http://phylo.wikidot.com/example-biogeobears-scripts#manual_modify_states

Re-using the manually modified of states_list
http://phylo.wikidot.com/example-biogeobears-scripts#reuse_modified_states

Manually modify the states list in time-stratified analyses
http://phylo.wikidot.com/example-biogeobears-scripts#modified_states_stratified

Cheers,

Nick

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