cov_D1st

pybrops.model.vmat.util.cov_D1st(r, nself, t)

Calculate a D1 matrix.

This matrix represents the covariance between genomic loci caused by linkage disequilibrium.

Parameters:

• r (numpy.ndarray) – Recombination probability matrix.

• nself (int, inf) –

  Selfing generation number to derive gametes from.

  Example	Description
  nself = 0	Derive gametes from F1
  nself = 1	Derive gametes from F2
  nself = 2	Derive gametes from F3
  ...	etc.
  nself = inf	Derive gametes from SSD

  Remark:

  • ’s’ takes priority over ‘t’. If s > 0, ‘t’ calculations are not performed.

• t (int, inf) –

  Random intermating generation number to derive gametes from.

  Example	Description
  t = 0	Derive gametes from F1
  t = 1	Derive gametes from (F1 x F1)
  t = 2	Derive gametes from (F1 x F1) x (F1 x F1)
  ...	etc.
  t = inf	Derive gametes from unlimited random intermating

  Remark:

  • ’s’ takes priority over ‘t’. If s > 0, ‘t’ calculations are not performed.

Returns:

D_1 – A D_1 matrix.

Return type:

numpy.ndarray