Compare one tree's quartets against others'

CompareQuartetsMulti() counts how many quartets in one tree are resolved in the same way or different ways in a forest of comparison trees.

CompareQuartetsMulti(x, cf)

Arguments

x

Object of class phylo representing the tree of interest.

cf

Comparison tree of class phylo, or list thereof, each with the same leaves as x.

Value

CompareQuartetsMulti() returns a named integer vector specifying the number of quartets whose resolution in x matches all or any of the resolutions in cf.

Named elements are:

N

The total number of quartet statements for the given number of n-leaf trees, i.e. n_trees × Q.

Q

The total number of quartets for n leaves.

s_all

The number of quartets that are resolved identically in all trees.

s_any

The number of quartets that are resolved in x, and identically in at least one of cf.

d_all

The number of quartets that are resolved in every tree in cf, but never in the same way as they are resolved in in x.

d_any

The number of quartets in x that are resolved differently (i.e. contradicted) in at least one tree in cf.

r1_all

The number of quartets that are resolved in x, but not in any of cf.

r1_any

The number of quartets that are resolved in x, but unresolved in at least one of cf.

r2_all

The number of quartets that are resolved in all of cf, but not in x.

r2_any

The number of quartets that are resolved in at least one of cf, but not in x.

u_all

The number of quartets that are unresolved in all trees.

u_any

The number of quartets that are unresolved in x and at least one tree in cf.

x_only

The number of quartets in x that are not resolved the same way in any of cf.

Details

CompareQuartetsMulti() explicitly evaluates each quartet in each tree. As such its runtime will increase hyper-exponentially with the number of leaves in trees being compared. 30 leaves will take around 5 seconds; 40 closer to 20 s, and 50 around a minute.

See also

Other element-by-element comparisons: CompareQuartets(), CompareSplits(), PairSharedQuartetStatus(), QuartetState(), SharedQuartetStatus(), SplitStatus()

Other quartet counting functions: AllQuartets(), CompareQuartets(), ResolvedQuartets()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

library("TreeTools")
CompareQuartetsMulti(x  = CollapseNode(as.phylo(42, 6), 8:9),
                     cf = list(BalancedTree(6), PectinateTree(6), 
                               CollapseNode(as.phylo(1337, 6), 9:10)))
#>      N      Q  s_all  s_any  d_all  d_any r1_all r1_any r2_all r2_any  u_all 
#>     60     15      0      4      4      9      0      7      1      3      0 
#>  u_any x_only 
#>      2      8