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Normalize tree distances

Source: R/tree_distance_utilities.R
NormalizeInfo.Rd

NormalizeInfo() is an internal function used to normalize information against a reference, such as the total information present in a pair of trees.

Usage

NormalizeInfo(
  unnormalized,
  tree1,
  tree2,
  InfoInTree,
  infoInBoth = NULL,
  how = TRUE,
  Combine = "+",
  ...
)

Arguments

unnormalized

Numeric value, vector or matrix to be normalized.

tree1, tree2

Trees from which unnormalized was calculated.

InfoInTree

Function to calculate the information content of each tree.

infoInBoth

Optional numeric specifying information content of both trees independently. If unspecified (NULL), this will be calculated using the method specified by how.

how

Method for normalization, perhaps specified using the normalize argument to a tree distance function. See details for options.

...

Additional parameters to InfoInTree() or how().

Value

NormalizeInfo() returns an object corresponding to the normalized values of unnormalized.

Details

The unnormalized value(s) are normalized by dividing by a denominator calculated based on the how parameter. Valid options include:

FALSE

No normalization is performed; the unnormalized values are returned.

TRUE

Unless infoInBoth is specified, the information in each tree is computed using InfoInTree(), and the two values combined using Combine().

A numeric value, vector or matrix

how is used as the denominator; the returned value is unnormalized / how.

A function

Unless infoInBoth is specified, the information in each tree is computed using InfoInTree(), and the two values combined using how. NormalizeInfo(how = Func) is thus equivalent to NormalizeInfo(how = TRUE, Combine = Func).

Author

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

Examples

library("TreeTools", quietly = TRUE)
pair1 <- c(BalancedTree(9), StarTree(9))
pair2 <- c(BalancedTree(9), PectinateTree(9))

# We'll let the number of nodes define the total information in a tree
Nnode(pair1)
#> [1] 8 1
Nnode(pair2)
#> [1] 8 8

# Let's normalize a unit distance
rawDist <- cbind(c(1, 1), c(1, 1))

# With `Combine = "+"`, the maximum distance is the sum of
# the information in each tree
denominator <- outer(Nnode(pair1), Nnode(pair2), "+")

NormalizeInfo(rawDist, pair1, pair2, InfoInTree = ape::Nnode, Combine = "+")
#>           [,1]      [,2]
#> [1,] 0.0625000 0.0625000
#> [2,] 0.1111111 0.1111111
rawDist / denominator
#>           [,1]      [,2]
#> [1,] 0.0625000 0.0625000
#> [2,] 0.1111111 0.1111111


# A denominator can be specified manually using `how`:
NormalizeInfo(rawDist, pair1, pair2, InfoInTree = ape::Nnode, how = 16)
#>        [,1]   [,2]
#> [1,] 0.0625 0.0625
#> [2,] 0.0625 0.0625
rawDist / 16
#>        [,1]   [,2]
#> [1,] 0.0625 0.0625
#> [2,] 0.0625 0.0625


# `how` also allows the denominator to be computed from trees:
outer(Nnode(pair1), Nnode(pair2), pmin)
#>      [,1] [,2]
#> [1,]    8    8
#> [2,]    1    1
NormalizeInfo(rawDist, pair1, pair2, InfoInTree = ape::Nnode, how = pmin)
#>       [,1]  [,2]
#> [1,] 0.125 0.125
#> [2,] 1.000 1.000
rawDist / outer(Nnode(pair1), Nnode(pair2), pmin)
#>       [,1]  [,2]
#> [1,] 0.125 0.125
#> [2,] 1.000 1.000