cladesub: substitute a clade with another clade replaces a specified...
In JeffWeinell/misc.wrappers: Miscellaneous Wrapper Functions for Spatial Population Genomics
cladesub R Documentation
substitute a clade with another clade
replaces a specified crown clade in a tree with a specified crown clade from a second tree.
Description
substitute a clade with another clade
replaces a specified crown clade in a tree with a specified crown clade from a second tree.
Usage
cladesub(tree1, tree2, tips1, tips2 = NULL, use.stem = "tree1")
Arguments
tree1
phylo object containing the clade that will be replaced
tree2
phylo object containing the replacement clade; if tips2 is NULL, then tree2 must be rooted
tips1
vector with tip names in tree1 with MRCA defining the clade to be replaced
tips2
NULL (default) or a vector with tip names in tree2 with MRCA defining the replacement clade; if NULL, then tree2 is the replacement clade.
use.stem
One of "tree1", "tree2", or "diff" (Default "tree1"). Determines the stem branch length of the substitute clade on the output tree. Setting to "tree1" or "tree2" uses the stem branch length of the clade to be replaced on tree1 or the replacement clade on tree2, respectively.
Value
phylo object
JeffWeinell/misc.wrappers documentation built on Sept. 20, 2023, 12:42 p.m.
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| cladesub | R Documentation |
substitute a clade with another clade replaces a specified crown clade in a tree with a specified crown clade from a second tree.
Description
substitute a clade with another clade
replaces a specified crown clade in a tree with a specified crown clade from a second tree.
Usage
cladesub(tree1, tree2, tips1, tips2 = NULL, use.stem = "tree1")
Arguments
tree1 |
phylo object containing the clade that will be replaced |
tree2 |
phylo object containing the replacement clade; if tips2 is NULL, then tree2 must be rooted |
tips1 |
vector with tip names in tree1 with MRCA defining the clade to be replaced |
tips2 |
NULL (default) or a vector with tip names in tree2 with MRCA defining the replacement clade; if NULL, then tree2 is the replacement clade. |
use.stem |
One of "tree1", "tree2", or "diff" (Default "tree1"). Determines the stem branch length of the substitute clade on the output tree. Setting to "tree1" or "tree2" uses the stem branch length of the clade to be replaced on tree1 or the replacement clade on tree2, respectively. |
Value
phylo object
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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