Description Usage Arguments Value
It calls C++ routine that implements the methodology of Hidden Markov Models (HMM) to construct multipoint linkage maps in outcrossing species
1 2 3 4 5 6 7 8 9  est_map_hmm_out(
geno,
error,
type,
phase,
rf.vec = NULL,
verbose = TRUE,
tol = 1e06
)

geno 
matrix of genotypes. Rows represent marker and columns represent individuals. 
type 
a vector indicating the type of marker. For more
information see 
phase 
a vector indicating the linkage phases between
markers. For more information see

rf.vec 
a vector containing the recombination fraction initial values 
verbose 
If 
tol 
tolerance for the C routine, i.e., the value used to evaluate convergence. 
a list containing the reestimated vector of recombination fractions and the logarithm of the likelihood
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