get.rate.matrix: Create a CTMC rate matrix from rasters and parameter...

Description Usage Arguments Details Value Author(s) References Examples

View source: R/get.rate.matrix.R

Description

Creates a CTMC rate matrix from rasters and parameter estimates (perhaps from a GLM analysis).

Usage

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get.rate.matrix(object, stack.static, stack.grad,
    normalize.gradients = FALSE, grad.point.decreasing = TRUE,
    directions=4, zero.idx=integer(), coef)

Arguments

object

A fitted GLM or GAM object used to fit the CTMC movement model

stack.static

A rasterStack object, where each layer in the stack is a location-based covariate.

stack.grad

A rasterStack object, where each layer in the stack is a directional gradient-based covariate

normalize.gradients

Logical. Default is FALSE. If TRUE, then all gradient covariates are normalized by dividing by the length of the gradient vector at each point.

grad.point.decreasing

Logical. If TRUE, then the gradient covariates are positive in the direction of decreasing values of the covariate. If FALSE, then the gradient covariates are positive in the direction of increasing values of the covariate (like a true gradient).

directions

Integer. Either 4 (indicating a "Rook's neighborhood" of 4 neighboring grid cells) or 8 (indicating a "King's neighborhood" of 8 neighboring grid cells).

zero.idx

Integer vector of the indices of raster cells that are not passable and should be excluded. These are cells where movement should be impossible. Default is zero.idx=integer().

coef

A vector of coefficents to use in place of those in 'object'

Details

This function takes the covariate rasters in stack.static (motility covariates) and stack.grad (gradient covariates) and creates a CTMC rate matrix defining movement between all neighboring raster grid cells. It is NOT possible to include an autocovariate here ("crw" in ctmc2glm). If such was included in the original fitted model, then the crw term is set equal to zero.

Value

An n-by-n Matrix of CTMC rate values.

Author(s)

Ephraim M. Hanks

References

Hanks, E. M.; Hooten, M. B. & Alldredge, M. W. Continuous-time Discrete-space Models for Animal Movement. The Annals of Applied Statistics, 2015, 9, 145-165

Examples

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## For example code, do
##
## > help(ctmcMove)

Example output

Loading required package: raster
Loading required package: sp
Loading required package: Matrix
Loading required package: fda
Loading required package: splines

Attaching package: 'fda'

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

    matplot

Loading required package: gdistance
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


Attaching package: 'gdistance'

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

    normalize

ctmcmove documentation built on April 20, 2018, 5:03 p.m.