Description Usage Arguments Details Value References Examples
Given two species abundance matrices (of possibly unequal size), find nearest species compositional neighbors.
1  nearestspecies(spe1, spe2, method, ties = FALSE, ...)

spe1 
species abundance matrix with greater number of sites (rows) 
spe2 
species abundance matrix with lesser number of sites (rows) 
method 
dissimilarity index, per

ties 
logical, should ties (nonunique values) be allowed?
default is 
... 
additional arguments passed to function 
Useful to subset the longer of two datasets for analyses that
require compatible dimensions (e.g.,
mantel
, procrustes
).
If ties = FALSE
, then all returned values are unique;
if ties = TRUE
, then unique values are not enforced, so
any sample unit in spe1
may be picked repeatedly.
Example of first use is in Smith and Gray (2018).
Numeric vector indexing rows (sample units) in spe1
which
are nearest compositional neighbors of spe2
. The order
corresponds to row order in spe2
.
Smith, R. J., and A. N. Gray. 2018. Combining potentially incompatible community datasets when harmonizing forest inventories in subarctic Alaska. Journal of Vegetation Science: accepted.
1 2 3 4 5 6 7 8 9 10 11 12 13 14  # two candidate datasets, full and partial
set.seed(181)
data(smoky)
full < smoky$spe
part < (full + abs(rnorm(prod(dim(full)), 0, 25)))[1:6,]
# subset the full matrix, based on compositional nearest neighbors
i < nearestspecies(full, part, ties=FALSE)
i
full < full[i,,]
# default is to break ties
nearestspecies(full, part, ties=FALSE)
nearestspecies(full, part, ties=TRUE)

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