All functions

MphCalcLogL()

Calculate log likelihood

MphEM()

Perform expectation-maximization algorithm to infer Vg and Ve values for a pair of traits.

UpdateRL_B()

Update B for restricted log likelihood

calc_XHiY()

Calculate XHiY

calc_omega()

Calculate Omega matrices

calc_qi()

Calculate Qi (inverse of Q) and log determinant of Q

calc_sigma()

Calculate Sigma_ee and Sigma_uu matrices

center_kinship()

Center a relatedness matrix, after Zhou's GEMMA function CenterMatrix

eigen2()

Calculate eigendecomposition and return ordered eigenvalues and eigenvectors

eigen_proc()

Eigendecomposition procedure for Vg and Ve

gemma2

gemma2

stagger_mats()

Stagger matrices within a larger, block-diagonal matrix

update_e()

Update E

update_u()

Update U matrix

update_v()

Update V_e and V_g