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Allow for genetic value tracking in the multivariate case #175

Merged
merged 15 commits into from Jan 18, 2019
Merged

Allow for genetic value tracking in the multivariate case #175

merged 15 commits into from Jan 18, 2019

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molpopgen
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@molpopgen molpopgen commented Jan 9, 2019 •
edited

Builds on #164 and #172 to allow multivariate genetic values to be tracked during simulation for all dimensions.

  • Add matrix types to C++ classes
  • Add ndarray properties to Python classes
  • Add simulation support
  • Add tracking for ancient samples
  • Serialization of the new data fields in the population class
  • Determine if we can maintain backwards compatibility with the previous serialization format.
  • Add documentation to manual re: new matrix types

@molpopgen molpopgen added this to the 0.3.0 milestone Jan 9, 2019
@molpopgen
Add new header file for returning numpy views of std::vector. #147
0f7d683
@molpopgen
Change calls to make_1d_ndarray to refer to namespace. Include new
6790c26 
header file.
@molpopgen
Add vectors to contain genetic value matrices for the current pop
12c31e2 
plus ancient samples.
@molpopgen
Expose the genetic value matrix types to Python. Currently, this
99c2c77 
is done as a 1d array.
@molpopgen
Add make_2d_ndarray
750bc9b
@molpopgen
Change the new matrices to 2d arrays as properties and add docstrings.
cba697a
@molpopgen
Add support for tracking the genotype matrix array during tree sequence
0c758a9 
simulations.
@molpopgen
Add recording of genotype matrix data for ancient samples.
8223ace
@molpopgen
remove unused variable
18d834d
@molpopgen
Make updating the genetic values matrix optional for simulations
0ad5bfb 
with tree sequence recording.
@molpopgen
Add record_gvalue_matrix option to the Python function for tree sequence
1e3de71 
recording.
@molpopgen
remove print statement
eb1dbf2
@molpopgen molpopgen merged commit 61fbace into dev Jan 18, 2019
@molpopgen molpopgen deleted the multivariate_gvalue_tracking branch February 14, 2019 21:02
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