getBiprts: Get the sets of labels for each bipartition in tree

In treeman: Phylogenetic Tree Manipulation Class and Methods

Description

Returns a list of tip IDs for each branch in the tree. Options allow the user to act as if the root is not present and to use a universal code for comparing between trees.

Usage

getBiprts(tree, tips = tree@tips, root = TRUE, universal = FALSE)

Arguments

tree	TreeMan object
tips	vector of tips IDs to use for bipartitions
root	Include the root for the bipartitions? Default TRUE.
universal	Create a code for comparing between trees

Details

Setting root to FALSE will ignore the bipartitions created by the root. Setting universal to TRUE will return a vector of 0s and 1s, not a list of tips. These codes will always begin with 1, and will allow for the comparison of splits between trees as they do not have "chiralty", so to speak.

See Also

calcDstRF

Examples

library(treeman)
tree <- randTree(10)
# get all of the tip IDs for each branch in the rooted tree
(getBiprts(tree))
# ignore the root and get bipartitions for unrooted tree
(getBiprts(tree, root = FALSE))
# use the universal code for comparing splits between trees
(getBiprts(tree, root = FALSE, universal = TRUE))

Example output

$n1
$n1[[1]]
 [1] "t1"  "t10" "t2"  "t3"  "t4"  "t5"  "t6"  "t7"  "t8"  "t9" 

$n1[[2]]
character(0)


$n2
$n2[[1]]
[1] "t1"  "t10" "t2"  "t5"  "t6"  "t7"  "t9" 

$n2[[2]]
[1] "t3" "t4" "t8"


$n3
$n3[[1]]
[1] "t3" "t4" "t8"

$n3[[2]]
[1] "t1"  "t10" "t2"  "t5"  "t6"  "t7"  "t9" 


$n4
$n4[[1]]
[1] "t1"  "t10" "t5"  "t7" 

$n4[[2]]
[1] "t2" "t3" "t4" "t6" "t8" "t9"


$n5
$n5[[1]]
[1] "t1" "t5" "t7"

$n5[[2]]
[1] "t10" "t2"  "t3"  "t4"  "t6"  "t8"  "t9" 


$n6
$n6[[1]]
[1] "t1" "t5"

$n6[[2]]
[1] "t10" "t2"  "t3"  "t4"  "t6"  "t7"  "t8"  "t9" 


$n7
$n7[[1]]
[1] "t2" "t6" "t9"

$n7[[2]]
[1] "t1"  "t10" "t3"  "t4"  "t5"  "t7"  "t8" 


$n8
$n8[[1]]
[1] "t2" "t6"

$n8[[2]]
[1] "t1"  "t10" "t3"  "t4"  "t5"  "t7"  "t8"  "t9" 


$n9
$n9[[1]]
[1] "t4" "t8"

$n9[[2]]
[1] "t1"  "t10" "t2"  "t3"  "t5"  "t6"  "t7"  "t9" 


$n2
$n2[[1]]
[1] "t1"  "t10" "t2"  "t5"  "t6"  "t7"  "t9" 

$n2[[2]]
[1] "t3" "t4" "t8"


$n3
$n3[[1]]
[1] "t3" "t4" "t8"

$n3[[2]]
[1] "t1"  "t10" "t2"  "t5"  "t6"  "t7"  "t9" 


$n4
$n4[[1]]
[1] "t1"  "t10" "t5"  "t7" 

$n4[[2]]
[1] "t2" "t3" "t4" "t6" "t8" "t9"


$n5
$n5[[1]]
[1] "t1" "t5" "t7"

$n5[[2]]
[1] "t10" "t2"  "t3"  "t4"  "t6"  "t8"  "t9" 


$n6
$n6[[1]]
[1] "t1" "t5"

$n6[[2]]
[1] "t10" "t2"  "t3"  "t4"  "t6"  "t7"  "t8"  "t9" 


$n7
$n7[[1]]
[1] "t2" "t6" "t9"

$n7[[2]]
[1] "t1"  "t10" "t3"  "t4"  "t5"  "t7"  "t8" 


$n8
$n8[[1]]
[1] "t2" "t6"

$n8[[2]]
[1] "t1"  "t10" "t3"  "t4"  "t5"  "t7"  "t8"  "t9" 


$n9
$n9[[1]]
[1] "t4" "t8"

$n9[[2]]
[1] "t1"  "t10" "t2"  "t3"  "t5"  "t6"  "t7"  "t9" 


[1] "1110011101" "1100010100" "1000010100" "1000010000" "1101110110"
[6] "1101110111" "1111011101"

treeman documentation built on July 8, 2020, 7:28 p.m.