[R] Speed up R code

[AnnaFowler]

Hi, Im new to R and having some trouble with my code - it works, its just
very slow! Ive tried lots of things, but nothing quite seems to work, so any
help and suggestions would be really appreciated!

I want to calculate the marginal likelihood for every element of a row of a
matrix and the corresponding element in every other row. Then sum these for
each row, so I get an upper triangular matrix which consists of the sum of
the marginal likelihoods for row i and row j. 


X<-read.table()
X1<-as.matrix(X)

mlr<-function(X1,p,q,Vinv=1){
X2<-X1^2
  P<-length(p)
  Q<-length(q)

  Res<-matrix(ncol=P,nrow=P)

  for(i in 1:(P-1)){

      lpi<-p[i]
        Y1<-matrix(nrow=(P-i),ncol=Q)
        Y2<-matrix(nrow=(P-i),ncol=Q)
        tB<-matrix(nrow=(P-i),ncol=Q)

         for(j in (i+1):P){
         lpj<-p[j]
         for(k in 1:Q){
            Y1[j-i,k]<-sum(X1[c(i,j),k])
            Y2[j-i,k]<-sum(X2[c(i,j),k])
            
            }
           tB[j-i,]<-(lpi+lpj)*q
          }
        
        V1<- (Vinv + tB)^(-1)
        c<-tB/2
        a1<-1 + c
        b1<-1 + (Y2 - V1*(Y1^2))/2
       z<-log(V1)/2 + lgamma(a1) - c*log.pi - a1*log(b1)
       Res[i,]<-c(rep(NA,i),apply(z,1,sum))
  }
  return(Res)
}


Its fine for a matrix of 100x100, but the data Im working with is 3538x116,
and so this can take hours!

Any help would be really appreciated!
Thanks,
Anna
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