mantel.correlog function

Mantel (cross-)correlograms

mantel.correlog is the function to calculate a Mantel (cross-)correlogram. The function requires two (or three) matrices.

mantel.correlog(
  dmat,
  zmat,
  wmat = NULL,
  increment,
  resamp = 999,
  quiet = FALSE
)

Arguments

• dmat: a matrix representing distance.
• zmat: a matrix representing similarity.
• wmat: an optional third matrix of similarities to calculate a Mantel cross-correlograms.
• increment: increment for the uniformly distributed distance classes.
• resamp: the number of permutations under the null to assess level of significance.
• quiet: If TRUE, the counter is suppressed during execution.

Returns

An object of class "correlog" is returned, consisting of the following components: - correlation: the value for the Moran (or Mantel) similarity.

• mean.of.class: the actual average of the distances within each distance class.

• nlok: the number of pairs within each distance class.

• x.intercept: the interpolate x.intercept of Epperson (1993).

• p: the permutation two-sided p-value for each distance-class.

• corr0: If a cross-correlogram is calculated, corr0 gives the empirical cross-correlation at distance zero.

Details

The function calculates Mantel (cross-)correlograms at discrete distance classes from two (or three) matrixes. The first is the matrix of distances and the second is a matrix of similarities. The optional third matrix is an additional similarity matrix to be used to calculate a Mantel cross-correlogram. Missing values are allowed -- values are assumed missing at random.

Examples

# first generate some sample data
x <- expand.grid(1:20, 1:5)[, 1]
y <- expand.grid(1:20, 1:5)[, 2]

# z data from an exponential random field
z <- cbind(
  rmvn.spa(x = x, y = y, p = 2, method = "exp"), 
  rmvn.spa(x = x, y = y, p = 2, method = "exp")
  )

# w data from a gaussian random field
w <- cbind(rmvn.spa(
  x = x, y = y, p = 2, method = "gaus"), 
  rmvn.spa(x = x, y = y, p = 2, method = "gaus")
  )

# Make distance and similarity matrices
zmat <- cor(t(z))
wmat <- cor(t(w))
dmat <- sqrt(outer(x, x, "-")^2 + outer(y, y, "-")^2)

# Mantel correlogram 
fit1 <- mantel.correlog(dmat = dmat, zmat = zmat, increment = 2, quiet = TRUE, 
                        resamp = 0)
## Not run: plot(fit1)
# Mantel cross-correlogram 
fit2 <- mantel.correlog(dmat = dmat, zmat = zmat, wmat = wmat, increment = 2, 
                        quiet = TRUE, resamp = 0)
## Not run: plot(fit2)

See Also

plot.correlog

Author(s)

Ottar N. Bjornstad onb1@psu.edu