transition: Create an object of the class Transition

In gdistance: Distances and Routes on Geographical Grids

Description

Create a Transition object from a RasterLayer or RasterBrick object. Transition values are calculated with a user-defined function from the grid values.

Usage

transition (x, transitionFunction, directions, ...)

Arguments

x	RasterLayer or RasterBrick (raster package)
transitionFunction	Function to calculate transition values from grid values
directions	Directions in which cells are connected (4, 8, 16, or other), see adjacent
...	additional arguments, see methods 1 and 3 below

Details

Users may use one of three methods to construct a Transition* object with this function.

1) TransitionLayer from RasterLayer

transition(x, transisitonFunction, directions, symm)

When a symmetric transition matrix is required, the user should supply a transitionFunction f that obeys f(i,j) = f(j,i) (a commutative function). The function transition does no commutativity check. To obtain an asymmetric transition matrix, a non-commutative function should be supplied and an additional argument ‘symm’ should be set to FALSE.

2) TransitionLayer from RasterBrick

transition(x, transitionFunction="mahal", directions)

This method serves to summarize several layers of data in a single distance measure. The distance between adjacent cells is the normalized reciprocal of the Mahalanobis distance (mean distance / (mean distance + distance ij).

3) TransitionStack from RasterLayer

In contrast with the above methods, this method produces resistance matrices by default.

a) Continuous variables - barriers

transition(x, transitionFunction="barriers", directions, symm, intervalBreaks)

This method creates a TransitionStack with each layer containing a discrete boundary between areas in x. Areas are defined by intervals in x. The argument intervalBreaks is a vector of interval breaks corresponding to the values in x. If between a pair of cells i and j, min(i,j) < break AND max(i,j) > break, then the value ij in the transition matrix becomes 1. All other values in the transition matrix remain 0. The package classInt offers several methods to define intervals. If symm is changed from the default (TRUE) to "up" or "down", it will give either only the upslope (symm="up") or downslope (symm="down") barriers.

b) Categorical variables - barriers

transition(x, transitionFunction="barriers", directions)

In this case, areas are defined as categories in the input raster. A raster with a categorical variable can be created with asFactor(). The layers of the resulting TransitionStack contain all possible combinations of categories. Which layer contains the combination of categories i and j out of n categories, can be determined with these formulae:

if symm is TRUE: layer(i,j) = n*(j-1) - j*(j-1)/2 + i-j. if symm is FALSE and i>j: layer(i,j) = ((n*(j-1) - j*(j-1)/2 + i-j) * 2) - 1. if symm is FALSE and i<j: layer(i,j) = (n*(j-1) - j*(j-1)/2 + i-j) * 2.

c) Categorical variables - areas

transition(x, transitionFunction="areas", directions)

Here, areas are also a categorical variable (see under 3b). The layers in the resulting TransitionStack represent each one area. Connections between two cells which are each inside the area are set to 1. Connections between a cell inside and a cell outside the area are set to 0.5. Connections between two cells outside the area are set to 0.

Value

Transition object

Author(s)

Jacob van Etten [e-mail]

Examples

  #Create a new raster and set all its values to unity.
  r <- raster(nrows=18, ncols=36) 
  r <- setValues(r, runif(ncell(r)))

  #Create a Transition object from the raster
  tr <- transition(r, transitionFunction=mean, directions=4)
  tr #the sparse matrix is of class dsCMatrix (symmetric)

  #Create an asymmetric transition matrix
  #first, an arbitrary non-commutative function 
  f <- function(x) max(x) - x[1] + x[2] 
  tr2 <- transition(r, f, 4, symm=FALSE)
  tr2 #the sparse matrix is of class dgCMatrix (=asymmetric)
  
  #Barriers - interval breaks
  tr3 <- transition(r, "barriers", 8, intervalBreaks=c(0.25, 0.5, 0.75))
  nlayers(tr3)

  #Barriers - categories
  r <- round(r * 2)
  r <- asFactor(r)
  tr4 <- transition(r, "barriers", 8)
  nlayers(tr4)
  plot(raster(tr4[[2]]))
  
  #Areas
  r <- round(r * 2)
  r <- asFactor(r)
  tr5 <- transition(r, "areas", 8)
  nlayers(tr5)
  plot(raster(tr5[[2]]))

Example output

Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:raster':

    union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: Matrix

Attaching package: 'gdistance'

The following object is masked from 'package:igraph':

    normalize

class       : TransitionLayer 
dimensions  : 18, 36, 648  (nrow, ncol, ncell)
resolution  : 10, 10  (x, y)
extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 
values      : conductance 
matrix class: dsCMatrix 
class       : TransitionLayer 
dimensions  : 18, 36, 648  (nrow, ncol, ncell)
resolution  : 10, 10  (x, y)
extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 
values      : conductance 
matrix class: dgCMatrix 
[1] 3
[1] 3
[1] 3

gdistance documentation built on May 2, 2019, 5:46 p.m.