gdistance (version 1.6.4)

pathInc: Incidence of paths from a common origin: overlap and non-overlap

Description

Calculate the overlap and non-overlap of paths departing from a common origin. Two algorithms are available: random walk and randomised shortest paths.

Usage

pathInc(x, origin, from, to, theta, weight, ...)

Value

list of dist objects or list of matrices

Arguments

x

transition matrix of class Transition*

origin

coordinates of the origin (one point location, SpatialPoints, matrix or numeric class)

from

coordinates of the destinations (SpatialPoints, matrix or numeric class)

to

second set of coordinates of the destinations (can be missing)

theta

value > 0 and < 20 (randomised shortest paths) or missing (random walk)

weight

matrix – Reciprocals of the non-zero values are used as weights. If missing, reciprocals of the transition matrix are used.

...

additional arguments passed to methods. See Details.

Author

Jacob van Etten. Implementation of randomised shortest paths based on Matlab code by Marco Saerens.

Details

This is a complex wrapper function that calculates to what extent dispersal routes overlap or do not overlap.

First, the function calculates the trajectories for all "from" and "to" locations, starting from a single "origin" location. These trajectories can either be based on random walks or randomised shortest paths (giving a value to theta).

Then, for all unique pairs of trajectories, it calculates the extent to which these trajectories overlap or diverge. These values are given back to the user as a list of (distance) matrices.

If only "from" coordinates are given, the function calculates symmetric distance matrices for all combinations of points in "from". If both "from" and "to" coordinates are given, the function calculates a matrix of values with rows for all locations in "from" and columns for all locations in "to".

Overlap is currently calculated as the minimum values of each pair of trajectories compared. Non-overlap uses the following formula: Nonoverlap = max(0,max(a,b)*(1-min(a,b))-min(a,b)) (see van Etten and Hijmans 2010). See the last example to learn how to use an alternative function.

References

McRae B.H., B.G. Dickson, and T. Keitt. 2008. Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 89:2712-2724.

Saerens M., L. Yen, F. Fouss, and Y. Achbany. 2009. Randomized shortest-path problems: two related models. Neural Computation, 21(8):2363-2404.

van Etten, J., and R.J. Hijmans. 2010. A geospatial modelling approach integrating archaeobotany and genetics to trace the origin and dispersal of domesticated plants. PLoS ONE 5(8): e12060.

Examples

library("raster")
library("sp")

# Create TransitionLayer
r <- raster(ncol=36,nrow=18)
r <- setValues(r,rep(1,times=ncell(r)))
tr <- transition(r,mean,directions=4)

# Two different types of correction are required
trR <- geoCorrection(tr, type="r", multpl=FALSE)
trC <- geoCorrection(tr, type="c", multpl=FALSE)

# Create TransitionStack
ts <- stack(trR, trR)

# Points for origin and coordinates between which to calculate path (non)overlaps
sP0 <- SpatialPoints(cbind(0,0))
sP1 <- SpatialPoints(cbind(c(65,5,-65),c(-55,35,-35)))

# Randomised shortest paths
# rescaling is needed: exp(-theta * trC) should give reasonable values
# divide by median of the non-zero values
trC <- trC / median(transitionMatrix(trC)@x)
pathInc(trC, origin=sP0, from=sP1, theta=2)

# Random walk
pathInc(trR, origin=sP0, from=sP1)

# TransitionStack as weights
pathInc(trR, origin=sP0, from=sP1, weight=ts)

# Demonstrate use of an alternative function
#The current default is to take the minimum of each pair of layers

altoverlap <- function(a, b)
{
  aV <- as.vector(a[,rep(1:ncol(a), each=ncol(b))])
  bV <- as.vector(b[,rep(1:ncol(b), times=ncol(a))])
  result <- matrix(aV * bV, nrow = nrow(a), ncol=ncol(a)*ncol(b))
  return(result)
}

pathInc(trR, origin=sP0, from=sP1, weight=ts, functions=list(altoverlap))