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.
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.
Examples
tree <- randTree(10)
# get all of the tip IDs for each branch in the rooted tree
(getBiprts(tree))
#> $n1
#> $n1[[1]]
#> [1] "t1" "t10" "t2" "t3" "t4" "t5" "t6" "t7" "t8" "t9"
#>
#> $n1[[2]]
#> character(0)
#>
#>
#> $n2
#> $n2[[1]]
#> [1] "t10" "t2" "t4" "t5" "t7" "t8"
#>
#> $n2[[2]]
#> [1] "t1" "t3" "t6" "t9"
#>
#>
#> $n3
#> $n3[[1]]
#> [1] "t1" "t3" "t6" "t9"
#>
#> $n3[[2]]
#> [1] "t10" "t2" "t4" "t5" "t7" "t8"
#>
#>
#> $n4
#> $n4[[1]]
#> [1] "t3" "t6"
#>
#> $n4[[2]]
#> [1] "t1" "t10" "t2" "t4" "t5" "t7" "t8" "t9"
#>
#>
#> $n5
#> $n5[[1]]
#> [1] "t1" "t9"
#>
#> $n5[[2]]
#> [1] "t10" "t2" "t3" "t4" "t5" "t6" "t7" "t8"
#>
#>
#> $n6
#> $n6[[1]]
#> [1] "t2" "t4" "t7" "t8"
#>
#> $n6[[2]]
#> [1] "t1" "t10" "t3" "t5" "t6" "t9"
#>
#>
#> $n7
#> $n7[[1]]
#> [1] "t2" "t4" "t8"
#>
#> $n7[[2]]
#> [1] "t1" "t10" "t3" "t5" "t6" "t7" "t9"
#>
#>
#> $n8
#> $n8[[1]]
#> [1] "t2" "t4"
#>
#> $n8[[2]]
#> [1] "t1" "t10" "t3" "t5" "t6" "t7" "t8" "t9"
#>
#>
#> $n9
#> $n9[[1]]
#> [1] "t10" "t5"
#>
#> $n9[[2]]
#> [1] "t1" "t2" "t3" "t4" "t6" "t7" "t8" "t9"
#>
#>
# ignore the root and get bipartitions for unrooted tree
(getBiprts(tree, root = FALSE))
#> $n2
#> $n2[[1]]
#> [1] "t10" "t2" "t4" "t5" "t7" "t8"
#>
#> $n2[[2]]
#> [1] "t1" "t3" "t6" "t9"
#>
#>
#> $n3
#> $n3[[1]]
#> [1] "t1" "t3" "t6" "t9"
#>
#> $n3[[2]]
#> [1] "t10" "t2" "t4" "t5" "t7" "t8"
#>
#>
#> $n4
#> $n4[[1]]
#> [1] "t3" "t6"
#>
#> $n4[[2]]
#> [1] "t1" "t10" "t2" "t4" "t5" "t7" "t8" "t9"
#>
#>
#> $n5
#> $n5[[1]]
#> [1] "t1" "t9"
#>
#> $n5[[2]]
#> [1] "t10" "t2" "t3" "t4" "t5" "t6" "t7" "t8"
#>
#>
#> $n6
#> $n6[[1]]
#> [1] "t2" "t4" "t7" "t8"
#>
#> $n6[[2]]
#> [1] "t1" "t10" "t3" "t5" "t6" "t9"
#>
#>
#> $n7
#> $n7[[1]]
#> [1] "t2" "t4" "t8"
#>
#> $n7[[2]]
#> [1] "t1" "t10" "t3" "t5" "t6" "t7" "t9"
#>
#>
#> $n8
#> $n8[[1]]
#> [1] "t2" "t4"
#>
#> $n8[[2]]
#> [1] "t1" "t10" "t3" "t5" "t6" "t7" "t8" "t9"
#>
#>
#> $n9
#> $n9[[1]]
#> [1] "t10" "t5"
#>
#> $n9[[2]]
#> [1] "t1" "t2" "t3" "t4" "t6" "t7" "t8" "t9"
#>
#>
# use the universal code for comparing splits between trees
(getBiprts(tree, root = FALSE, universal = TRUE))
#> [1] "1001001001" "1110110111" "1000000001" "1101011001" "1101011101"
#> [6] "1101011111" "1011101111"