Check Explicit Tree Link Metadata

Summarize whether otu_tree_link or taxa_tree_link is structurally consistent with the current object.

Usage

check_tree_link(object, tree = c("otu_tree", "taxa_tree"))

Arguments

object

A microbiome_dataset object.

tree

Tree slot, either "otu_tree" or "taxa_tree".

Value

A one-row data frame summarizing coverage and potential issues.

Examples

data("global_patterns", package = "microbiomedataset")

x <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:120])
x <- microbiomedataset::convert2microbiome_dataset(
  microbiomedataset::convert2phyloseq(x)
)
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
check_tree_link(x, tree = "taxa_tree")
#>        tree has_tree has_link n_links linked_variables uncovered_variables
#> 1 taxa_tree     TRUE     TRUE     120              120                   0
#>   invalid_nodes duplicated_variables
#> 1             0                    0