DPhyloStatistic: D-Statistic for Binary States on a Phylogeny

In npcooley/SynExtend: Tools for Working With Synteny Objects

D-Statistic for Binary States on a Phylogeny

Description

Calculates if a presence/absence pattern is random, Brownian, or neither with respect to a given phylogeny.

Usage

DPhyloStatistic(dend, PAProfile, NumIter = 1000L)

Arguments

dend	An object of class dendrogram
PAProfile	A vector representing presence/absence of binary traits. See Details for more information.
NumIter	Number of iterations to simulate for random permutation analysis.

Details

This function implements the D-Statistic for binary traits on a phylogeny, as introduced in Fritz and Purvis (2009). The statstic is the following ratio:

\frac{D_{obs} - D_b}{D_r - D_b}

Here D_{obs} is the D value for the input data, D_b is the value under simulated Brownian evolution, and D_r is the value under random permutation of the input data. The D value measures the sum of sister clade differences in a phylogeny weighted by branch lengths. A score close to 1 indicates phylogenetically random distribution, and a score close to 0 indicates the trait likely evolved under Brownian motion. Scores can fall outside this range; these scores are only intended as benchmark points on the scale. See the original paper cited in References for more information.

The input PAProfile supports a number of formatting options:

• Character vector, where each element is a label of the dendrogram. Presence in the character vector indicates presence of the trait in the corresponding label.

• Integer vector of length equivalent to the number of leaves, comprised of 0s and 1s. 0 indicates absence in the corresponding leaf, and 1 indicates presence.

• Logical vector of length equivalent to number of leaves. FALSE indicates absence in the corresponding leaf, and TRUE indicates presence.

See Examples for a demonstration of each case.

Value

Returns a numerical value. Values close to 0 indicate random distribution, and values close to 1 indicate a Brownian distribution.

Author(s)

Aidan Lakshman [e-mail]

References

Fritz S.A. and Purvis A. Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits. Conservation Biology, 2010. 24(4):1042-1051.

Examples

##########################################################
### Replicating results from Table 1 in original paper ###
##########################################################

# creates a dendrogram with 16 leaves and branch lengths all 1
distMat <- suppressWarnings(matrix(seq_len(17L), nrow=16, ncol=16))
testDend <- as.dendrogram(hclust(as.dist(distMat)))
testDend <- dendrapply(testDend, \(x){
                      attr(x, 'height') <- attr(x, 'height') / 2
                      return(x)
                    })
attr(testDend[[1]], 'height') <- attr(testDend[[2]], 'height') <- 3
attr(testDend, 'height') <- 4
plot(testDend)

set.seed(123)

# extremely clumped (should be close to -2.4)
DPhyloStatistic(testDend, as.character(1:8))

# clumped Brownian (should be close to 0)
DPhyloStatistic(testDend, as.character(c(1,2,5,6,10,12,13,14)))

# random (should be close to 1.0)
DPhyloStatistic(testDend, as.character(c(1,4:6,10,13,14,16)))

# overdispersed (should be close to 1.9)
DPhyloStatistic(testDend, as.character(seq(2,16,by=2)))

###########################################
### Different ways to create PAProfiles ###
###########################################

allLabs <- as.character(labels(testDend))

# All these ways create a PAProfile with
# presence in members 1:4
# and absence in members 5:16

# numeric vector:
c(rep(1,4), rep(0, length(allLabs)-4))

# logical vector:
c(rep(TRUE,4), rep(FALSE, length(allLabs)-4))

# character vector:
allLabs[1:4]

npcooley/SynExtend documentation built on Nov. 15, 2024, 3:02 p.m.