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############################################################################
## methods ##
############################################################################
##' Methods for dealing with objects containing taxonomic information
##' (Taxonomy, TNRS endpoints)
##'
##' This is the page for the generic methods. See the help pages for
##' \code{\link{taxonomy_taxon_info}}, \code{\link{taxonomy_mrca}}, and
##' \code{\link{tnrs_match_names}} for more information.
##'
##' @title Methods for Taxonomy
##' @param tax an object returned by \code{\link{taxonomy_taxon_info}},
##' \code{\link{taxonomy_mrca}}, or \code{\link{tnrs_match_names}}
##' @param ... additional arguments (see
##' \code{\link{tnrs_match_names}})
##' @rdname taxonomy-methods
##' @export
tax_rank <- function(tax, ...) {
UseMethod("tax_rank")
}
##' @export
##' @rdname taxonomy-methods
ott_id <- function(tax, ...) {
UseMethod("ott_id")
}
##' @export
##' @rdname taxonomy-methods
synonyms <- function(tax, ...) {
UseMethod("synonyms")
}
##' @export
##' @rdname taxonomy-methods
tax_sources <- function(tax, ...) UseMethod("tax_sources")
##' @export
##' @rdname taxonomy-methods
is_suppressed <- function(tax, ...) UseMethod("is_suppressed")
##' @export
##' @rdname taxonomy-methods
unique_name <- function(tax, ...) UseMethod("unique_name")
##' @export
##' @rdname taxonomy-methods
tax_name <- function(tax, ...) UseMethod("tax_name")
### flags -----------------------------------------------------------------------
##' @export
##' @rdname match_names-methods
flags <- function(tax, ...) UseMethod("flags")
###
##' Retrieve the detailed information for the list of studies used in
##' the Tree of Life.
##'
##' @title List of studies used in the Tree of Life
##'
##' @details This function takes the object resulting from
##' \code{tol_about(study_list = TRUE)}, \code{tol_mrca()},
##' \code{tol_node_info()}, and returns a data frame listing the
##' \code{tree_id}, \code{study_id} and \code{git_sha} for the
##' studies currently included in the Tree of Life.
##'
##' @param tax a list containing a \code{source_id_map} slot.
##' @param ... additional arguments (currently unused)
##'
##' @return a data frame
##' @export
source_list <- function(tax, ...) UseMethod("source_list")
##' Extract the lineage information (higher taxonomy) from an object
##' returned by \code{\link{taxonomy_taxon_info}}.
##'
##' The object passed to this function must have been created using
##' the argument \code{include_lineage=TRUE}.
##'
##' @title Lineage of a taxon
##' @param tax an object created by \code{\link{taxonomy_taxon_info}}
##' using the argument \code{include_lineage=TRUE}.
##' @param ... additional arguments (currently unused).
##' @return A list with one slot per taxon that contains a data frame
##' with 3 columns: the taxonomy rank, the name, and unique name
##' for all taxa included in the lineage of the taxon up to the
##' root of the tree.
##' @rdname tax_lineage
##' @export
tax_lineage <- function(tax, ...) UseMethod("tax_lineage")
##' @export
##' @rdname tol_node_info
tol_lineage <- function(tax, ...) UseMethod("tol_lineage")
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