nQuackEMstep_Breakdown

 # Input data setup - this is not kmers, but your allele frequencies (which you labeled `temp`)
 xm <- as.matrix(temp)
 xi <- (xm[,2]/xm[,1])
 
 # Other variables
 trunc = c(0.0,0.0)
 niter = 1000
 epsilon = 0.1
 parmlist = list(avec = c(0.33, 0.33, 0.33), mvec = c(0.25, 0.50, 0.75), svec = c(0.01, 0.01,0.01))  #This is your expected for your tetraploid


saveme <- emstepNA(parmlist = parmlist, xi = xi, niter = niter, epsilon = epsilon, trunc = trunc, type = "fixed")

Update with 1.0.5

Input data setup - this is not kmers, but your allele frequencies (which you labeled temp)

xm <- as.matrix(temp)
xi <- (xm[,2]/xm[,1])

Other variables

trunc = c(0.0,0.0)
niter = 1000
epsilon = 0.1
parmlist = list(avec = c(0.33, 0.33, 0.33), mvec = c(0.25, 0.50, 0.75), svec = c(0.01, 0.01,0.01)) #This is your expected for your tetraploid

saveme <- emstepNA(parmlist = parmlist, xi = xi, niter = niter, epsilon = epsilon, trunc = trunc, type = "fixed", glreturn = TRUE)
gpmatrix <- saveme$pir