letsR (version 4.0)

lets.overlap: Compute pairwise species' geographic overlaps

Description

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.

See Also

lets.presab

lets.presab.birds

Examples

# NOT RUN {
data(PAM)
CZ <- lets.overlap(PAM, method = "Chesser&Zink")
prop <- lets.overlap(PAM, method = "Proportional")
cells <- lets.overlap(PAM, method = "Cells")
# }
# NOT RUN {
   
# }