examples/dsdive.obsld.R

In jmhewitt/dsdive: Discrete Space Models for Dive Trajectories of Animals

library(dsdive)
data('dive.sim')
attach(dive.sim)
attach(dive.sim$params)

# extract time between observations
tstep = diff(sim.obs$times[1:2])

# get true stage transition times
t.stages = sim$times[c(FALSE, diff(sim$stages)==1)]

# build probability matrices for observations
obstx.mat = lapply(1:3, function(s) {
  dsdive.obstx.matrix(depth.bins = depth.bins, beta = dive.sim$params$beta, 
                      lambda = lambda, 
                      s0 = s, tstep = tstep, include.raw = TRUE, delta = 1e-10)
})

# compute likelihood of observations, given model parameters
ld = dsdive.obsld(dsobs.list = list(sim.obs,sim.obs),
                  t.stages.list = list(t.stages,t.stages), 
                  P.raw = obstx.mat, s0 = 1, sf = 3)

detach(dive.sim$params)
detach(dive.sim)