polyDist {treenomial}

Calculates the distance between coefficient matrices

Description

Calculates the distance between two coefficient matrices or a coefficient matrix and a list of coefficient matrices.

Usage

polyDist(
  x,
  Y,
  method = c("fraction", "logDiff", "wLogDiff", "pa", "ap"),
  numThreads = -1
)

Arguments

x

single coefficient matrix to find distances to

Y

a list of coefficient matrices

method

method to use when calculating coefficient distances:

“fraction”

for two coefficient matrices A and B returns sum(abs(A-B)/(A+B)), excluding elements where both A and B are zero

“logDiff”

for two coefficient matrices A and B returns sum(log(1+abs(A-B))

“wLogDiff”

performs the “logDiff” method with weights on the rows

“pa”

total pairs where the coefficient is present in one matrix and absent in the other (presence-absence)

“ap”

opposite comparison of pa (absence-presence)

numThreads

number of threads to be used, the default (-1) will use the number of cores in the machine and numThreads = 0 will only use the main thread

Value

vector of distances

Note

• the substituted y coefficient vector only supports the “logDiff” method and the “fraction” method

• “pa” and “ap” force symmetry in the output distance matrix

Examples

library(treenomial)
library(ape)

# distance between coefficient matrices of one 10 tip tree
# and 100 trees with 30 tips using
# create the coefficient matrices
tenTipTree <- rtree(10)
tenTipTreeCoeff <- treeToPoly(tenTipTree, numThreads = 0)

thirtyTipList <- rmtree(100, 30)
thirtyTipCoeffs <- treeToPoly(thirtyTipList, numThreads = 0)

# find the distance
polyDist(tenTipTreeCoeff, thirtyTipCoeffs, numThreads = 0)