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Okay, now I'm trying it on 5.8.9. I'm seeing two issues:
- t/error_interruption.t has the exact same issue that 5.10 has (see #18).
- t/override_errors.t has some bizarre thing going on where some of…
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Some sections of the documentation on using BAMMtools needs to be finished.
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R functions for summarizing rates etc for speciationextinction model but I don't think they are yet finished for trait evolution.
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Need a subset bammdata function that pulls out a SUBTREE from bammdata object. Maybe name is subtreeBAMM.
E.g for a given node x, the everything except stuff pertaining to this subtree is discarded fr…
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More params to deprecate, now from all the Trait-associated classes (plus Settings):
acceptrateOutfile
nodeStateOutfile
updateRateNumberTimeVariablePartitions
I have no idea what this param does an…
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I'm just flagging this as an issue, but sphinx doc is not finished and this should stay open until it is done.
Also, even when done, we will need to go through all the example code and make sure it c…
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I'm getting a seg fault with bamm traits again. Here is output from gdb.
pascals-mbp:test pascaltitle$ gdb ./bamm
GNU gdb (GDB) 7.6.1
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+:…
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Have arg ephy take either bamm-data or bamm-ratematrix datattypes. should check, then (if bamm-data) call getRateThroughTimeMatrix. otherwise, use the already-computed rate-through-time matrix. Users …
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unless someone has already started documenting things I'd suggest we hold off on package skeleton. I also think we should talk about who documents what and how to document things consistently.
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Quit and warn if trees contain polytomies and/or are non-ultrametric.