make_matrix_X_l.RdHa! I did this initially using R straight up and even tried to make it reasonably vectorized, but the damn thing took forever and was incredible space-inefficient. Ergo, we are going after it using Rcpp. The genotypes are ordered in rows and columns in the way as described in the paper.
make_matrix_X_l(p, kappa)vector of allele frequencies
a 3-vector of the Cotterman coefficients