loglik <-function(theta,spdata,covariates){
#loglik <- function(theta, tracks,corridor. = corridor, patch. = patch, di. = di){
#To be updated: include spdata and covariates as inputs for function
# theta = parameters;
# ta = tracks;
# corridor/patch = matrix of habitat type (0/1);
# di = matrix of distances
alpha <- exp(theta[1])
betaC <- theta[2]
betaP <- theta[3]
li <- 0
idt <- tracks[,2]
uid <- unique(idt)
ta <- tracks[,3]
for(ss in 1:length(uid)){ #for each one of the tracks
lta <- ta[idt==uid[ss]] #data for the focal track
for(i in 1:(length(lta)-1)){ #for each movement step
x <- lta[i]
pr <- exp(-di.[x,]/alpha) * exp(betaC * corridor.) * exp(betaP * patch.)
pr <- pr / sum(pr)
pr <- pr + 10^(-10) # is this really necesary?
pr <- pr / sum(pr)
li <- li + log(pr[lta[i + 1]])
}
}
return(li)
}
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