"sim.conn" <- function(Eall,N,prop,rconn,beta) { nA <- as.integer(prop*N) nB <- N-nA denom <- beta*nA^2*rconn - beta*nA*rconn + beta*nA*nB + rconn*nA*nB - rconn*nB + nB^2 pA <- rconn*beta*N*Eall/denom pB <- -N*Eall*(rconn-nA*rconn-nB+beta*nA)/(nB-1)/denom pAB <- beta*N*Eall/denom MBp <- new("MBparams") MBp <- addParams(x=MBp,N=N,m=2) MBp <- calcSim(x=MBp,func=sim.thresh,pNum=2) MBp@Sim[[1]] <- matrix(0,N,N) MBp@Sim[[1]][1:nA,1:nA][upper.tri(MBp@Sim[[1]][1:nA,1:nA])] <- rbinom(choose(nA,2),1,pA) MBp@Sim[[1]][1:nA,(nA+1):N] <- rbinom(nA*nB,1,pAB) MBp@Sim[[1]][(nA+1):N,(nA+1):N][upper.tri(MBp@Sim[[1]][(nA+1):N,(nA+1):N])] <- rbinom(choose(nB,2),1,pB) MBp@Sim[[1]] <- MBp@Sim[[1]]+t(MBp@Sim[[1]]) MBp@Sim[[1]] <- as.matrix.csr(MBp@Sim[[1]]) return(MBp) }