evalBranch | R Documentation |
This function evaluates the effect of modifying a single branch length on Phylogenetic Diversity (PD) and the selection of sets with the highest PD. It allows for both decreasing (to zero) and increasing (to a user-defined maximum).
evalBranch(
tree = tree,
distribution = distribution,
branchToEval = "terminals",
approach = "upper",
root = FALSE,
index = "PD",
maxMultiplier = 1.01,
redondeo = 3,
verbose = FALSE,
compact = TRUE,
printNames = FALSE
)
tree |
A single phylogenetic tree in APER format. |
distribution |
A matrix indicating the distribution of terminal taxa across sets. |
branchToEval |
The branch(es) to evaluate (can be a numeric vector of node numbers, "terminals", "internals", or "all", default = "terminals"). |
approach |
The type of branch length modification: "lower" (decrease to zero), "upper" (increase to maximum), or "all" for both (default = "upper"). |
root |
Logical indicating whether to use the root in PD calculation (default = FALSE). |
index |
The index used for PD calculation (e.g., "PD"). |
maxMultiplier |
Multiplier for determining the upper limit of branch length modification (BL_sum * maxMultiplier, default = 1.01). |
redondeo |
Number of decimal places for rounding. |
verbose |
Logical indicating whether to print verbose output (default = FALSE). |
compact |
Logical indicating whether to return a compact output (default = TRUE). |
printNames |
Logical indicating whether to print terminal names in output. |
The function returns a list containing information about the effect of branch length modifications on set selection, including:
'branchToEval': The evaluated branch(es).
'bestInitialArea': The set(s) with the highest PD in the initial tree.
'bestModifiedArea': The set(s) with the highest PD in the modified tree.
'approach': The type of branch length modification used.
'delta': The percentage change in branch length.
'initialPD': The initial PD value.
'modifiedPD': The PD value after the branch length modification.
'initialLength': The initial branch length.
'finalLength': The final branch length after modification.
'areas': A vector of set names.
'terminals': A vector of terminal taxa names.
'root': Logical indicating whether the root was used in PD calculation.
'index': The PD index used.
Miranda-Esquivel Daniel R.
library(blepd)
data(tree)
data(distribution)
# Evaluate the effect of increasing the length of terminal branches
result_upper <- evalBranch(tree = tree, distribution = distribution,
branchToEval = "terminals", approach = "upper")
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