dsdive.obsld: Likelihood for collection of partially observed dives

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

Description

Likelihood for collection of partially observed dives

Usage

dsdive.obsld(dsobs.list, t.stages.list, P.raw, s0, sf)

Arguments

dsobs.list	list of dsobs objects, which describe the observation times and depths of a collection of dives
t.stages.list	list of stage transition times for dives observed in dsobs.list
P.raw	list of continuous time probability transition matrices, and components.
s0	likelihood should include contributions for stages greater or equal to s0
sf	likelihood should include contributions for stages less than or equal to sf

Examples

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)

jmhewitt/dsdive documentation built on May 29, 2020, 5:18 p.m.