ecodist (version 1.00)

mgram: Mantel correlogram

Description

Calculates simple and partial Mantel correlograms.

Usage

mgram(species.d, space.d, nclass, stepsize, nperm = 1000, mrank = FALSE, nboot = 500, pboot = 0.9, cboot = 0.95, alternative = "two.sided", trace = FALSE)

Arguments

species.d

lower-triangular dissimilarity matrix.

space.d

lower-triangular matrix of geographic distances.

nclass

number of distance classes. If not specified, Sturge's rule will be used to determine an appropriate number of classes.

stepsize

width of each distance class. If not specified, nclass and the range of space.d will be used to calculate an appropriate default.

nperm

number of permutations to use. If set to 0, the permutation test will be omitted.

mrank

if this is set to F (the default option), Pearson correlations will be used. If set to T, the Spearman correlation (correlation ranked distances) will be used.

nboot

number of iterations to use for the bootstrapped confidence limits. If set to 0, the bootstrapping will be omitted.

pboot

the level at which to resample the data for the bootstrapping procedure.

cboot

the level of the confidence limits to estimate.

alternative

default is "two.sided", and returns p-values for H0: rM = 0. The alternative is "one.sided", which returns p-values for H0: rM

trace

if TRUE, returns progress indicators.

Value

• Returns a matrix with one row for each distance class and 6 columns:
• dmax
  upper limit of the distance class.
• ngroup
  number of distances in that class.
• mantelr
  Mantel r value.
• pval
  p-value for the test chosen.
• llim
  lower bound of confidence limit for mantelr.
• ulim
  upper bound of confidence limit for mantelr.

Details

This function calculates Mantel correlograms. The Mantel correlogram is essentially a multivariate autocorrelation function. The Mantel r represents the dissimilarity in variable composition (often species composition) at a particular lag distance.

References

Legendre, P. and M. Fortin. 1989. Spatial pattern and ecological analysis. Vegetatio 80:107-138.

See Also

mantel, plotmgram, pmgram

Examples

z.mgram <- mgram(z.d, space.d)
plotmgram(z.mgram)

# A full example is available in the Mantel correlogram 
# section of the main help file for \link{ecodist}.