allProbs: Matrix of all probabilities In TheoMichelot/moveHMM: Animal Movement Modelling using Hidden Markov Models

Description

Used in functions `viterbi`, `logAlpha`, `logBeta`.

Usage

 ```1 2``` ```allProbs(data, nbStates, stepDist, angleDist, stepPar, anglePar = NULL, zeroInflation = FALSE, knownStates = NULL) ```

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 distribution is not estimated. `zeroInflation` `TRUE` if the step length distribution is inflated in zero. Default: `FALSE`. `knownStates` Vector of values of the state process which are known prior to fitting the model (if any). Default: NULL (states are not known). This should be a vector with length the number of rows of 'data'; each element should either be an integer (the value of the known states) or NA if the state is not known.

Value

Matrix of all probabilities.

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12``` ```## Not run: 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) ## End(Not run) ```

TheoMichelot/moveHMM documentation built on Dec. 8, 2017, 3:08 p.m.