TEST2 {DNAseqtest} | R Documentation |
This function tests for symmetry between all the pairs of K matched DNA sequences.
TEST2(f)
f |
a |
This function calculates Bowker's test for symmetry, Stuart's test for
marginal symmetry and the test for internal symmetry. It depends on the 4^K
observed divergence array N.
A list of three lower triangle matrices
first |
the lower triangle of the matrix contains (K-1) x (K-1) values shows Bowker's test between all the possible pairs of the K sequences |
second |
the lower triangle of the matrix contains (K-1) x (K-1) values shows Stuart's test between all the possible pairs of the K sequences |
third |
the lower triangle of the matrix contains (K-1) x (K-1) values shows the internal test between all the possible pairs of the K sequences |
Lars Sommer Jermiin, Vivek Jayaswal, Faisal Ababneh, John Robinson (2008). Phylogenetic model evaluation. Bioinformatics, Volume 452 of the series Methods in Molecular Biology, 331-364.
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.
Ntml, simapp, simemb, TEST3
merge2<-matrix(c(-1,-4,-3,2,-2,-5,1,3), 4, 2)
theta<-c(rep(.25,3), rep(.25,3), rep(.25,3), c(.2,.35,.79,.01,.93,.47),
3,.1,.5,.8)
F1<-gn(theta,merge2)
N1<-Ntml(1000,F1)
t2<-TEST2(N1)
t2