Checks that phylogenetic trees are valid, parameters are in acceptable ranges, and the host-to-symbiont linking data frame has the correct structure.
Usage
check_inputs(
Host_tree,
Symbiont_tree,
Host_to_Symbiont_df,
min_hosts,
min_symbiont_tips,
span_fraction,
permutations
)Arguments
- Host_tree
A phylo object; binary phylogenetic tree of hosts
- Symbiont_tree
A phylo object; rooted, binary phylogenetic tree of symbionts. Rooting is required: see Details.
- Host_to_Symbiont_df
A data frame with columns "Host" and "Symbiont" that links each symbiont tip to the host it was isolated from
- min_hosts
Minimum number of hosts required for a node to be included in the scan; must be >= 3
- min_symbiont_tips
Minimum number of symbiont tips in a subtree; default 7 is recommended
- span_fraction
Fraction of total tree span; filters nodes with span <= this fraction of maximum span (0-1)
- permutations
Number of permutations for significance testing; default 99 recommended, higher values more accurate
Details
Symbiont_tree must be rooted. codiv() tests one clade per internal node,
so the rooting decides which clades exist to be tested. An unrooted tree read
by ape::read.tree() still has a node sitting in the root position, picked
by the order of the Newick string, so a scan would run and report an
arbitrary set of clades rather than failing. Root the tree before resolving
polytomies: ape::multi2di() applied to an unrooted tree splits the basal
polytomy with a zero-length branch, after which ape::is.rooted() returns
TRUE for a tree nobody rooted.
Examples
Host_tree <- ape::rtree(10)
Symbiont_tree <- ape::rtree(100)
Host_to_Symbiont_df <- data.frame(
"Host" = rep(Host_tree$tip.label, 10),
"Symbiont" = Symbiont_tree$tip.label
)
check_inputs(Host_tree, Symbiont_tree, Host_to_Symbiont_df, 4, 7, 0.25, 99)