Distances between each pair of trees — CompareAll • TreeDist

Calculate the distance between each tree in a list, and each other tree in the same list.

Usage

CompareAll(x, Func, FUN.VALUE = Func(x[[1]], x[[1]], ...), ...)

Arguments

x: List of trees, in the format expected by Func().
Func: distance function returning distance between two trees, e.g. path.dist().
FUN.VALUE: Format of output of Func(), to be passed to vapply(). If unspecified, calculated by running Func(x[[1]], x[[1]]).
...: Additional parameters to pass to Func().

Value

CompareAll() returns a distance matrix of class dist detailing the distance between each pair of trees. Identical trees are assumed to have zero distance.

Details

CompareAll() is not limited to tree comparisons: Func can be any symmetric function.

Author

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

Examples

# Generate a list of trees to compare
library("TreeTools", quietly = TRUE)
trees <- list(bal1 = BalancedTree(1:8), 
              pec1 = PectinateTree(1:8),
              pec2 = PectinateTree(c(4:1, 5:8)))

# Compare each tree with each other tree
CompareAll(trees, NNIDist)
#> $lower
#>      bal1 pec1 pec2
#> bal1         2    2
#> pec1    2         2
#> pec2    2    2     
#> 
#> $best_lower
#>      bal1 pec1 pec2
#> bal1         2    2
#> pec1    2         3
#> pec2    2    3     
#> 
#> $tight_upper
#>      bal1 pec1 pec2
#> bal1         2    2
#> pec1    2         3
#> pec2    2    3     
#> 
#> $best_upper
#>      bal1 pec1 pec2
#> bal1         2    2
#> pec1    2         3
#> pec2    2    3     
#> 
#> $loose_upper
#>      bal1 pec1 pec2
#> bal1         4    4
#> pec1    4         5
#> pec2    4    5     
#> 
#> $fack_upper
#>      bal1 pec1 pec2
#> bal1         4    4
#> pec1    4         5
#> pec2    4    5     
#> 
#> $li_upper
#>      bal1 pec1 pec2
#> bal1        10   10
#> pec1   10         8
#> pec2   10    8     
#> 
  
# Providing FUN.VALUE yields a modest speed gain:
dist <- CompareAll(trees, NNIDist, FUN.VALUE = integer(7))
  
# View distances as a matrix
as.matrix(dist$lower)
#>      bal1 pec1 pec2
#> bal1    0    2    2
#> pec1    2    0    2
#> pec2    2    2    0