#' Uses HW function to make matrix of genotype values per matrix
#'
#' Takes frequencies of resistant allele at each locus - user inputted
#' @param P_1 todo
#' @param P_2 todo
#'
#' @return matrix
#' @export
make.genotypemat <- function ( P_1, P_2 ){
#for locus 1
loc1 <- matrix(c(rep(0,3)), ncol=1)
loc1 <- HW( P_1, loc1 ) # Entered in order SS RS RR, found using P entered above
#for locus 2
loc2 <- matrix(c(rep(0,3)), ncol=1) #for locus 2
loc2 <- HW( P_2, loc2 ) # Entered in order SS RS RR, found using P entered above
mat <- matrix (c(rep(0,10)), ncol=1)
colnames(mat) <- "Freq."
rownames(mat) <- c("SS1SS2", "SS1RS2", "SS1RR2",
"RS1SS2", "RS1RS2_cis", "RS1RS2_trans", "RS1RR2",
"RR1SS2", "RR1RS2", "RR1RR2")
mat[1,] <- loc1[1,]*loc2[1,] ## locus 1 matrix SS, locus 2 matrix SS (always in row 1)
mat[2,] <- loc1[1,]*loc2[2,]
mat[3,] <- loc1[1,]*loc2[3,]
mat[4,] <- loc1[2,]*loc2[1,]
## two forms of RS1RS2
mat[5,] <- ( loc1[2,]*loc2[2,] ) * 0.5 #cis
mat[6,] <- ( loc1[2,]*loc2[2,] ) * 0.5 #trans
mat[7,] <- loc1[2,]*loc2[3,] ## locus 1 matrix RS, locus 2 matrix RR (always in rows 2 and 3 respectively)
mat[8,] <- loc1[3,]*loc2[1,]
mat[9,] <- loc1[3,]*loc2[2,]
mat[10,] <- loc1[3,]*loc2[3,]
return(mat)
}
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