initialize.x: Diagnose and initialize light level estimation.

In tripEstimation: Metropolis sampler and supporting functions for estimating animal movement from archival tags and satellite fixes

Description

Primarily for the purposes of initializing the estimation, these functions can also be used for diagnostic purposes. position.logp produces grids of simplistic position likelihood for each twilight and uses those to initialize positions for running estimations.

Usage

position.logp(model, x1, x2, xrest = NULL, subset = 1:model$n,
initialize.x = TRUE, start = NULL, end = NULL, prob = 0.8, winoffset = 5)

initialize.x(model, x1, x2, xrest = NULL)

light.quantile(model, chain, day, seg, probl = c(0.025, 0.5, 0.975))

show.segment(model, chain, segment, day, light, k, n = 50, ...)

Arguments

model	estimation model object
x1	vector of x-coordinates defining the prior grid
x2	vector of y-coordinates defining the prior grid
xrest	value for remaining parameters - default is light attenuation
subset	evaluate subset of segments - default uses all
initialize.x	logical - create initial points for x?
prob	probability - threshold to apply to overlapping quantiles, defaults to 0.8
winoffset	an odd-numbered window size to use when intersecting subseqent segments - defaults to 5

chain	chain object from estimation
day	POSIXct vector of date-times
seg	desired segment
probl	probability level for quantile
start	known position of release
end	known position of recapture

segment	vector of segment data
light	vector of light data
k	desired segment to show
n	length of vector to evaluate
...	additional arguments to be passed to plot

Details

The primary function here is position.logp, for initializing the estimation for solar.model and metropolis0.

Author(s)

Michael D. Sumner

tripEstimation documentation built on May 2, 2019, 4:59 p.m.