#'simSeqSample
#'
#'Simulates N single sequences with four possible states.
#'
#'
#'
#'@param trans a 4x4 matrix containing transition probabilities
#'@param initial a four element vector containing initial states probabilities
#'@param length single value specifying the length of the simulated sequence (columns)
#'@param N number of sequences which should be simulated (rows)
#'
#'
#'
#'@examples
#'
#' test1<-matrix(c(0.5 , 0.2 , 0.2 , 0.1,
#' 0.8 , 0.05, 0.05, 0.1,
#' 0.5 , 0.1 , 0.2 , 0.2,
#' 0.1 , 0.1 , 0.1 , 0.7) , 4 , 4 , byrow = TRUE)
#'
#' initial<-c(.25 , .25 , .25 , .25)
#'
#' simSeq(test1, initial, 30)
#'
#'@export
simSeqSample<-function(trans, initial, length, N){
comb<-simSeq(trans, initial, length)
#split
seq1<-c()
seq1[comb==1|comb==3]<-0
seq1[comb==2|comb==4]<-1
seq2<-c()
seq2[comb==1|comb==2]<-0
seq2[comb==3|comb==4]<-1
out<-c(seq1, seq2)
for(i in 2:N){
comb<-simSeq(trans, initial, length)
seq1[comb==1|comb==3]<-0
seq1[comb==2|comb==4]<-1
seq2[comb==1|comb==2]<-0
seq2[comb==3|comb==4]<-1
out<-rbind(out,c(seq1, seq2))
}
return(out)
}
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