nearestNeighborDist: Nearest Neighbor Distances for Morphological Disparity...
In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

nearestNeighborDist

R Documentation

Nearest Neighbor Distances for Morphological Disparity Studies

Description

This is a simple function for obtaining nearest neighbor distance from a symmetric pair-wises distance matrix, assumed here to be dissimilarities between pairs of taxa. Per-species NND is returned rather than a mean or other summary value.

Usage

nearestNeighborDist(distMat)

Arguments

distMat

A symmetric, square pair-wise distance matrix, assumed to be a dissimilarity matrix with a diagonal that is either zero values, NA values, or a mixture of both. Can be a 'dist' object rather than a numerical matrix. Taxon labels can be applied to the rows and columns (or as labels if a 'dist' object) and will be used to name the resulting output.

Details

This function is mainly included here for pedagogical (teaching) purposes. NND is so simple to calculate, users are urged to write their own functions for primary research purposes.

Typically, the mean NND for a group is reported and used to compare different groupings of taxa (such as different time intervals, or different clades). Bootstrapping should be used to generate confidence intervals.

Value

Returns a vector of the nearest neighbor distance for each unit (taxon) in the pair-wise distance matrix, named with the labels from the input distance matrix.

Author(s)

David W. Bapst

References

Bapst, D. W., P. C. Bullock, M. J. Melchin, H. D. Sheets, and C. E. Mitchell. 2012. Graptoloid diversity and disparity became decoupled during the Ordovician mass extinction. Proceedings of the National Academy of Sciences 109(9):3428-3433.

Ciampaglio, C. N., M. Kemp, and D. W. McShea. 2001. Detecting changes in morphospace occupation patterns in the fossil record: characterization and analysis of measures of disparity. Paleobiology 27(4):695-715.

Foote, M. 1990. Nearest-neighbor analysis of trilobite morphospace. Systematic Zoology 39:371-382.

Examples

#example using graptolite disparity data from Bapst et al. 2012

#load data
data(graptDisparity)

#calculate mean NND
NND <- nearestNeighborDist(graptDistMat)
mean(NND)

#calculate NND for different groups

#group (clade/paraclade) coding
groupID <- graptCharMatrix[,54]+1

groupNND <- numeric(7)
names(groupNND) <- c("Normalo.","Monogr.","Climaco.",
   "Dicrano.","Lasiogr.","Diplogr.","Retiol.")
for(i in unique(groupID)){
   groupNND[i] <- mean(nearestNeighborDist(
      graptDistMat[groupID == i,groupID == i]))
   }
groupNND

#the paraphyletic Normalograptids that survived the HME are most clustered
   #but this looks at all the species at once
   #and doesn't look for the nearest *co-extant* neighbor!
   #need to bring in temporal info to test that

dwbapst/paleotree documentation built on Aug. 30, 2022, 6:44 a.m.