R/exGen.R

In moveHMM: Animal Movement Modelling using Hidden Markov Models

#' Example data simulation
#'
#' Generate the file \code{data/example.RData}, used in other functions' examples and unit tests.

exGen <- function()
{
    set.seed(1)

    # simulate data
    nbAnimals <- 2
    nbStates <- 2
    nbCovs <- 2
    mu<-c(15,50)
    sigma<-c(10,20)
    angleMean <- c(pi,0)
    kappa <- c(0.7,1.5)
    stepPar <- c(mu,sigma)
    anglePar <- c(angleMean,kappa)
    stepDist <- "gamma"
    angleDist <- "vm"
    zeroInflation <- FALSE
    obsPerAnimal <- c(50,100)

    simPar <- list(nbAnimals=nbAnimals,nbStates=nbStates,angleMean=angleMean,stepDist=stepDist,
                   angleDist=angleDist,zeroInflation=zeroInflation)

    data <- simData(nbAnimals=nbAnimals,nbStates=nbStates,stepDist=stepDist,angleDist=angleDist,
                    stepPar=stepPar,anglePar=anglePar,nbCovs=nbCovs,zeroInflation=zeroInflation,
                    obsPerAnimal=obsPerAnimal)

    # estimate model
    mu0 <- c(20,70)
    sigma0 <- c(10,30)
    kappa0 <- c(1,1)
    stepPar0 <- c(mu0,sigma0)
    anglePar0 <- kappa0
    formula <- ~cov1+cos(cov2)
    nbCovs <- length(attr(terms(formula), "term.labels"))

    beta0 <- matrix(c(rep(-1.5,nbStates*(nbStates-1)),rep(0,nbStates*(nbStates-1)*nbCovs)),
                    nrow=nbCovs+1,byrow=TRUE)
    delta0 <- rep(1,nbStates)/nbStates

    par0 <- list(stepPar0=stepPar0,anglePar0=anglePar0,formula=formula,nbCovs=nbCovs,beta0=beta0,
                 delta0=delta0)

    m <- fitHMM(data=data,nbStates=nbStates,stepPar0=stepPar0,anglePar0=anglePar0,beta0=beta0,
                delta0=delta0,formula=formula,stepDist=stepDist,angleDist=angleDist,
                angleMean=angleMean)

    example <- list(data=data,m=m,simPar=simPar,par0=par0)
    save(example,file="data/example.RData")
}

# Roxygen documentation for the data file "data/example.RData"

#' Example dataset
#'
#' This data is generated by the function \code{\link{exGen}}, and used in the examples and tests of
#' other functions to keep them as short as possible.
#'
#' It is a list of the following objects:
#' \itemize{
#' \item \code{data} A \code{\link{moveData}} object
#' \item \code{m} A \code{\link{moveHMM}} object
#' \item \code{simPar} The parameters used to simulate \code{data}
#' \item \code{par0} The initial parameters in the optimization to fit \code{m}
#' }
#'
#' @name example
#' @usage example
#' @docType data
NULL