Compute pairwise species' geographic overlaps

Creates a species geographic overlap matrix from a Presence-absence matrix.

Usage

lets.overlap(pam, method = "Chesser&Zink", xy = NULL)

Arguments

pam: A presence-absence matrix (sites in rows and species in columns, with the first two columns containing the longitudinal and latitudinal coordinates, respectively), or an object of class PresenceAbsence.
method: The method used to calculate the overlap matrix. "Chesser&Zink" calculates the degree of overlap as the proportion of the smaller range that overlaps within the larger range (Chesser & Zink 1994). "Proportional" calculates the proportion of a range that overlaps another range, the resultant matrix is not symmetric. "Cells" will show the number of overlapping grid cells between a pair of species' ranges (same for both species in a pair), here the resultant matrix is symmetric.
xy: Logical, if TRUE the input matrix contains geographic coordinates in the first two columns.

References

Chesser, R. Terry, and Robert M. Zink. "Modes of speciation in birds: a test of Lynch's method." Evolution (1994): 490-497.

Barraclough, Timothy G., and Alfried P. Vogler. "Detecting the geographical pattern of speciation from species-level phylogenies." The American Naturalist 155.4 (2000): 419-434.

Author

Fabricio Villalobos & Bruno Vilela

Examples

if (FALSE) { # \dontrun{
data(PAM)
CZ <- lets.overlap(PAM, method = "Chesser&Zink")
prop <- lets.overlap(PAM, method = "Proportional")
cells <- lets.overlap(PAM, method = "Cells")
} # }