Feature and performance release.
Highlights
- Extended
genetic_valuewithlevel="individual"(default),level="node", andlevel="edge"to return genetic values for the corresponding entities. #189 - Added
edge_effectto compute introduced effects on edges #189 - Improved algorithm for
genetic_value. Traits with many rare causal sites may be much faster, but the time required for common variants still dominates #194. genetic_valueandsim_phenotypetake anum_threadsargument, dividing the causal sites between that many worker threads. The default of 0 does the work on the calling thread. Up to 3.4 times faster on four threads, and less on a tree sequence big enough that the per-thread arrays leave cache #194
Breaking changes
genetic_valueandedge_effectnow raise aValueErrorif asite_idin the trait dataframe is not a valid site ID in the tree sequence. Negative values previously wrapped around to the end of the site table #193
Documentation
- Added a worked example relating causal-allele effects, edge effects, and edge, node, and individual genetic values #189
- Clarified that tstrait currently uses a site-mode effect model #189