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Ancestral sample#22
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Ancestral sample
…n of the mutation in fwdpp vector (which in turn has the position and metadata info)
also reorder lines/spaces for clarity
shouldn't be necessary if arg_tracker is constructed with correct starting index (only needed for starting simulation with initialized tree as opposed to a blank simulation)
also fixes a couple of code comments
adding mutation and site tables using info from ancestry tracker and optional initial tree with metadata for each metadata for ancestry tracker is pickled fwdpy11 mutation type, default metadata for mutations from initial tree is added if none present (as would be if tree from msprime)
code in wfarg and setup commented out, removed in evolve_arg, README updated
provide an override variable to __call__ which overrides the gc interval and forces simplification
…test_evolve) edgesets to edges in test_evolve, import namedtuple, check to make sure mutation array has mutations, parantheses errors, small change to README, gitignore ignores pyc files, comment out async/queue functions in evolve_functions header, slight addendum to override parameter
Make sure breakpoints are generated
also added caculating time_appending back in
changes in fwdpy11 allow easy construction of fwdpy11 mutation type from unpickled metadata
use ancestry_processor's num_nodes to set next_index (if next_index == 0, initialize a tracker with newly created "parent" nodes)
msprime: for split populations, mutation rate was being set by final population 1 pop size instead of initial population pop 1 size, only affects Figure 2B,2D,2E 2E: simulations was being called with split-recovery model (which doesn't currently exist in fwdpy11 as of right now), should've been called with pure split model
…", "B" bold in neutral_2 plot
…package, use eta for Fst, add symbols for BGS plots, remove msprime results from plot2.pdf, put non-duplication msprime vs fwdpy11 into supplemental figure
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added 5 commits
December 5, 2019 03:04
…d theoretical expectation) and increasing pdf size for some of the plots
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reorganized ancestral sample branch