R/cal_likelihood.R

In YangLabHKUST/MR-APSS: The MRAPSS package implement the MR-APPSS approach to test for the causal effect of an exposure on a outcome disease.

# The function for calculating likelihood
cal_likeli <- function(hat.b, A, Var, S, C1, C2, pi0){

  S2 <- mapply(function(M1,M2){M1 +  A %*% M2 %*% t(A) }, M1=S, M2=Var)
  S2 = lapply(split(S2, col(S2)), function(x){matrix(x, nrow=2, ncol=2)})

  P1 =  mapply(mvtnorm::dmvnorm, x= hat.b,  sigma=S2)
  P2 =  mapply(mvtnorm::dmvnorm, x= hat.b,  sigma=S)

  #return likelihood
  return(sum(log(pi0 * P1/2/pnorm(C1) + (1-pi0) * P2/2/pnorm(C2))))

}