PopGenReport (version 2.1)

genleastcost: Least-cost path analysis based on a friction matrix

Description

This function calculates the pairwise distances (Euclidean, cost path distances and genetic distances) of populations using a friction matrix and a spatial genind object. The genind object needs to have coordinates in the same projected coordinate system as the friction matrix. The friction matrix can be either a single raster of a stack of several layers. If a stack is provided the specified cost distance is calculated for each layer in the stack. The output of this function can be used with the functions wassermann or lgrMMRR to test for the significance of a layer on the genetic structure.

Usage

genleastcost(cats, fr.raster, gen.dist, NN=NULL, pathtype="leastcost", 
plotpath=TRUE,theta=1)

Value

returns a list that consists of four pairwise distance matrixes (Euclidean, Cost, length of path and genetic) and the actual paths as spatial line objects.

Details

to be written

References

Cushman, S., Wasserman, T., Landguth, E. and Shirk, A. (2013). Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics. Diversity, 5(1), 51-72. Landguth, E. L., Cushman, S. A., Schwartz, M. K., McKelvey, K. S., Murphy, M. and Luikart, G. (2010). Quantifying the lag time to detect barriers in landscape genetics. Molecular ecology, 4179-4191. Wasserman, T. N., Cushman, S. A., Schwartz, M. K. and Wallin, D. O. (2010). Spatial scaling and multi-model inference in landscape genetics: Martes americana in northern Idaho. Landscape Ecology, 25(10), 1601-1612.

See Also

landgenreport, popgenreport, wassermann, lgrMMRR

Examples

glc <- genleastcost(cats=landgen, fr.raster=fric.raster, gen.dist="D", NN=8)
wassermann(eucl.mat = glc$eucl.mat, cost.mat = glc$cost.mats, gen.mat = glc$gen.mat)
lgrMMRR(gen.mat = glc$gen.mat, cost.mats = glc$cost.mats, eucl.mat = glc$eucl.mat)