#' convert expanded genotype array to contracted genotype array
#'
#' constructs genotypes given gametes
#' returns array of genotype frequencies
#' This is refactored from code in runModel()
#'
#' @param aLong array with frequencies of expanded genotypes
#'
#' @examples
#' #genotypesLong2Short()
#' @return array with frequencies of genotypes
#' @export
genotypesLong2Short <- function( aLong )
{
#to convert from this
#fGenotypeExpanded <- array_named(l1a1=c('S1','R1'),l1a2=c('S1','R1'),l2a1=c('S2','R2'),l2a2=c('S2','R2'))
#to this
genotypes <- c( "SS1SS2", "SS1RS2", "SS1RR2",
"RS1SS2", "RS1RS2_cis", "RS1RS2_trans", "RS1RR2",
"RR1SS2", "RR1RS2", "RR1RR2")
aShort <- array_named( genotypes=genotypes )
aShort["SS1SS2"] <- aLong['S1','S1','S2','S2']
aShort["SS1RS2"] <- aLong['S1','S1','S2','R2'] +
aLong['S1','S1','R2','S2']
aShort["SS1RR2"] <- aLong['S1','S1','R2','R2']
aShort["RS1SS2"] <- aLong['S1','R1','S2','S2'] +
aLong['R1','S1','S2','S2']
aShort["RS1RS2_cis"] <- aLong['S1','R1','S2','R2'] +
aLong['R1','S1','R2','S2']
aShort["RS1RS2_trans"] <- aLong['S1','R1','R2','S2'] +
aLong['R1','S1','S2','R2']
aShort["RS1RR2"] <- aLong['S1','R1','R2','R2'] +
aLong['R1','S1','R2','R2']
aShort["RR1SS2"] <- aLong['R1','R1','S2','S2']
aShort["RR1RS2"] <- aLong['R1','R1','S2','R2'] +
aLong['R1','R1','R2','S2']
aShort["RR1RR2"] <- aLong['R1','R1','R2','R2']
return(aShort)
}
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