safe_taxonomic_reduction {Claddis} | R Documentation |
Performs Safe Taxonomic Reduction (STR) on a character-taxon matrix.
safe_taxonomic_reduction(cladistic_matrix)
cladistic_matrix |
A character-taxon matrix in the format imported by read_nexus_matrix. |
Performs Safe Taxonomic Reduction (Wilkinson 1995).
If no taxa can be safely removed will print the text "No taxa can be safely removed", and the str_taxa
and removed_matrix
will have no rows.
NB: If your data contains inapplicable characters these will be treated as missing data, but this is inappropriate. Thus the user is advised to double check that any removed taxa make sense in the light of inapplicable states. (As far as I am aware this same behaviour occurs in the TAXEQ3 software.)
str_taxa |
A matrix listing the taxa that can be removed ( |
reduced_matrix |
A character-taxon matrix excluding the taxa that can be safely removed. |
removed_matrix |
A character-taxon matrix of the taxa that can be safely removed. |
Graeme T. Lloyd graemetlloyd@gmail.com
Wilkinson, M., 1995. Coping with abundant missing entries in phylogenetic inference using parsimony. Systematic Biology, 44, 501-514.
build_cladistic_matrix, compactify_matrix, prune_cladistic_matrix, safe_taxonomic_reinsertion, read_nexus_matrix, write_nexus_matrix, write_tnt_matrix
# Performs STR on the Gauthier 1986 dataset used in Wilkinson (1995): str_data <- safe_taxonomic_reduction(cladistic_matrix = gauthier_1986) # View deleted taxa: str_data$str_taxa # View reduced matrix: str_data$reduced_matrix # View removed matrix: str_data$removed_matrix