Nothing
### TODO: how to deal with missing meta slot elements???
### Right now the functions break when an otu doesn't have meta slot
#' get_taxa_meta
#'
#' Retrieve metadata of all species/otus otus (operational taxonomic units) included in the nexml
#' @param nexml a nexml object
#' @param what One of href, rel, id, or xsi:type
#' @return the list of metadata for each taxon
#' @seealso \code{\link{get_item}}
#' @keywords internal
#' @examples
#' \dontrun{
#' data(bird.orders)
#' birds <- add_trees(bird.orders)
#' birds <- taxize_nexml(birds, "NCBI")
#' RNeXML:::get_taxa_meta(birds)
#' RNeXML:::get_taxa_meta(birds, 'rel')
#' RNeXML:::get_taxa_meta(birds, 'id')
#' RNeXML:::get_taxa_meta(birds, 'xsi:type')
#' }
get_taxa_meta <-
function(nexml, what='href'){
out <- lapply(nexml@otus, function(otus)
# sapply(otus@otu, function(otu) slot(otu@meta, what)))
sapply(otus@otu, function(otu) slot(otu@meta[[1]], what)))
unname(unlist(out, recursive = FALSE))
}
get_otu_meta <- get_taxa_meta
#' get_taxa_meta_list
#'
#' Retrieve metadata of all species/otus otus (operational taxonomic units) included in the nexml
#' @param nexml a nexml object
#' @param what One of href, rel, id, or xsi:type
#' @return the list of metadata for each taxon
#' @seealso \code{\link{get_item}}
#' @keywords internal
#' @examples \dontrun{
#' data(bird.orders)
#' birds <- add_trees(bird.orders)
#' birds <- taxize_nexml(birds, "NCBI")
#' RNeXML:::get_taxa_meta_list(birds)
#' RNeXML:::get_taxa_meta_list(birds, 'rel')
#' RNeXML:::get_taxa_meta_list(birds, 'id')
#' RNeXML:::get_taxa_meta_list(birds, 'xsi:type')
#' }
get_taxa_meta_list <-
function(nexml, what='href'){
out <- lapply(nexml@otus, function(otus){
out <- sapply(otus@otu, function(otu) slot(otu@meta[[1]], what))
names(out) <- name_by_id(otus@otu)
out
})
names(out) <- name_by_id(nexml@otus)
out
}
get_otu_meta_list <- get_taxa_meta_list
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