moveHMM (version 1.0)

allProbs: Matrix of all probabilities

Description

Used in functions viterbi, logAlpha, logBeta.

Usage

allProbs(data, nbStates, stepDist, angleDist, stepPar, anglePar = NULL,
  zeroInflation = FALSE)

Arguments

data

Object moveData.

nbStates

Number of states of the HMM.

stepDist

Name of the distribution of the step lengths.

angleDist

Name of the distribution of the turning angles. Set to "none" if the angle distribution should not be estimated.

stepPar

Parameters of the step length distribution. Must be provided in a matrix with one row for each parameter (in the order expected by the pdf of stepDist), and one column for each state.

anglePar

Parameters of the turning angle distribution. Must be provided in a matrix with one row for each parameter (in the order expected by the pdf of angleDist), and one column for each state. Default: NULL ; if the turning angles dist

zeroInflation

TRUE if the step length distribution is inflated in zero. Default: FALSE.

Value

• Matrix of all probabilities.

Examples

stepPar <- c(1,10,1,5,0.2,0.3)
anglePar <- c(0,pi,0.5,2)
stepDist <- "gamma"
angleDist <- "vm"
data <- simData(nbAnimals=5,nbStates=2,stepDist=stepDist,angleDist=angleDist,stepPar=stepPar,
                 anglePar=anglePar,nbCovs=2,zeroInflation=TRUE)
P <- allProbs(data=data,nbStates=2,stepDist=stepDist,angleDist=angleDist,
               stepPar=matrix(stepPar,ncol=2,byrow=TRUE),anglePar=matrix(anglePar,ncol=2,
               byrow=TRUE),zeroInflation=TRUE)