negllik.xy: HMM line transect model likelihood with at least some forward...

In david-borchers/hmltm: Line transect estimation with hidden Markov availability models

HMM line transect model likelihood with at least some forward distances.

Description

Evaluates HMM line transect model likelihood with perpendicular and forward distance data.

Usage

negllik.xy(
  b,
  xy,
  FUN,
  models = list(y = NULL, x = NULL),
  pm,
  Pi,
  delta,
  theta.f,
  theta.b,
  W,
  ymax,
  dy,
  nx = 100,
  groupfromy = NULL
)

Arguments

b	likelihood function parameters.
xy	detections data, including x values for each detection and y values for some, plus any covariates in model).
FUN	detection hazard function name.
models	model specification, as in est.hmltm.
pm	state-dependent Bernoulli parameters.
Pi	Markov model transition probability matrix.
delta	Markov model stationary distribution.
theta.f	REDUNDANT must = 0.
theta.b	REDUNDANT must = 90.
W	perpendicular truncation distance for fitting.
ymax	forward distance by which detection hazard has fallen to zero.
dy	Markov model distance step size.
nx	number of x-values to use in evaluating detection function.
groupfromy	a forward distance (y) below which all y's are grouped into a single interval in the likelihood function (i.e. exact y,s < groupfromy are combined into an interval rather than passed as exact distances).

david-borchers/hmltm documentation built on Oct. 29, 2023, 9:07 p.m.