Example code: the elk data

This code can be used to reproduce the elk example described in the vignette.

# load package
library(moveHMM)

# read data from URL
trackData <- elk_data

# format data
trackData$Easting <- trackData$Easting/1000
trackData$Northing <- trackData$Northing/1000

# pre-process data
data <- prepData(trackData,type="UTM",coordNames=c("Easting","Northing"))

# plot data
plot(data,compact=T)

# summarize data
summary(data,details=T)

#######################
## Fit a 2-state HMM ##
#######################
# initial parameters
mu0 <- c(0.1,1)
sigma0 <- c(0.1,1)
zeromass0 <- c(0.05,0)
stepPar0 <- c(mu0,sigma0,zeromass0)
angleMean0 <- c(pi,0)
kappa0 <- c(1,1)
anglePar0 <- c(angleMean0,kappa0)

m <- fitHMM(data=data,nbStates=2,stepPar0=stepPar0,anglePar0=anglePar0,
             formula=~dist_water)


# compute the confidence intervals
conf <- CI(m)

# plot the fitted model for the first animal
plot(m,animals="elk-115")
# alternatively: plot(m,animals=1)

# compute the states sequence
states <- viterbi(m)

# compute the states probabilities
sp <- stateProbs(m)

# plot states sequence, and states probabilities for first elk
plotStates(m,animals="elk-115")

# compute and plot the pseudo-residuals
pr <- pseudoRes(m)
plotPR(m)

#######################
## Fit a 3-state HMM ##
#######################
# initial parameters
mu0 <- c(0.1,0.5,3)
sigma0 <- c(0.05,0.5,1)
zeromass0 <- c(0.05,0.0001,0.0001)
stepPar0 <- c(mu0,sigma0,zeromass0)
angleMean0 <- c(pi,pi,0)
kappa0 <- c(1,1,1)
anglePar0 <- c(angleMean0,kappa0)

m3 <- fitHMM(data=data,nbStates=3,stepPar0=stepPar0,anglePar0=anglePar0,
             formula=~dist_water)

# compare the AIC of the models
print(AIC(m,m3))