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

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

## Arguments

x RasterLayer or RasterBrick (raster package) Function to calculate transition values from grid values Directions in which cells are connected (4, 8, 16, or other), see adjacent additional arguments, passed to methods

## 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.