MphCalcLogL()

Calculate log likelihood 
MphEM()

Perform expectationmaximization 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, blockdiagonal matrix 
update_e()

Update E 
update_u()

Update U matrix 
update_v()

Update V_e and V_g 