Smatrix function

Symmetric Matrix S

This function calculates the symmetric matrix S.

Smatrix(s, pix)

Arguments

• s: a vector of variables containing the six free parameters in the S matrix
• pix: a vector giving the stationary probabilities for the four nucleotides A, C, G and T

Details

This function calculates the matrix S, which we used to calculate the rate matrix R.

Returns

A 4 x 4 symmetric matrix

References

Faisal Ababneh, Lars S Jermiin, Chunsheng Ma, John Robinson (2006). Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22(10), 1225-1231.

See Also

Pt, Fmatrix, gn ,gn2

Examples

s<-c(.1,.2,.3,.4,.5,.6)
pi<-c(.1,.1,.1,.7)
sm<-Smatrix(s, pi)
sm