Making a Taxa Table based on the result of function TPL for Phylomatic

Making taxa table for software Phylomatic, as "Family/Genus/species"

Usage

taxa.table(x, file = NULL, substitute.sp.white.space = "_")

Arguments

x: A data.frame generated by function TPL
file: A character string referring the name of the plain text file to be generated.
substitute.sp.white.space: The substitution symbol between the genus and specific epithet.

Value

Taxa table for software Phylomatic.

Details

x must be a data.frame generated by function TPL.

References

Webb, C. O. and M. J. Donoghue (2005). Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes 5(1): 181-183.

Author

Jinlong Zhang jinlongzhang01@gmail.com

Examples



sp <- c( "Ranunculus japonicus", "Anemone udensis", 
         "Ranunculus repens", "Ranunculus chinensis", 
         "Solanum nigrum", "Punica sp." ) 
res <- TPL(sp)
taxa.table(res)
#> [1] "Ranunculaceae/Ranunculus/Ranunculus_japonicus"
#> [2] "Ranunculaceae/Ranunculus/Ranunculus_repens"   
#> [3] "Ranunculaceae/Ranunculus/Ranunculus_chinensis"
#> [4] "Ranunculaceae/Anemone/Anemone_udensis"        
#> [5] "Solanaceae/Solanum/Solanum_nigrum"            
#> [6] "Lythraceae/Punica/Punica_sp."