FAD {QSutils} | R Documentation |
Computes the Functional Attribute Diversity as the sum of elements in the pairwise distance matrix.
FAD(dst)
dst |
A "dist" object or a symmetrical matrix with pairwise distances. |
A value that corresponds to the Functional Attribute Diversity. The sum of matrix elements.
Mercedes Guerrero-Murillo and Josep Gregori
Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.
# Create the object. filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils") lst <- ReadAmplSeqs(filepath,type="DNA") # Compute the DNA distance matrix. dst <- DNA.dist(lst$hseqs,model="N") FAD(dst)