profile_ll: Profile (concentrated) likelihood evaluation for GAI

In calliste-fagard-jenkin/GAI: Generalised Abundance Index for Seasonal Invertibrates

Profile (concentrated) likelihood evaluation for GAI

Description

A function which evaluations the profile negative log likelihood of our observed count data, given the user model specifications of a GAI model.

Usage

profile_ll(
  par,
  obs,
  skeleton,
  a_choice = "mixture",
  dist_choice = "P",
  spline_specs = list(df = 10, degree = 3),
  N = NULL,
  returnN = F,
  DMs = list(),
  returnA = F
)

Arguments

par	A vector of estimated parameters for the model
obs	A matrix of observations. Rows for sites and columns for occasions.
skeleton	The skeleton which tells this function how to relist the estimated parameters.
a_choice	The character name of the method used to estimate the seasonal trend. Either "mixture", "stopover" or "splines".
dist_choice	The distribution for the observed counts, can be "P" (poisson), "NB" (negative binomial), "ZIP" (zero inflated poisson)
spline_specs	A list containing the df (degrees of freedom) and the 'degree' for the splines.
N	optionally, instead of using the profile likelihood approach to estimate N (the superpopulation at each site), it can be supplied as a vector or integer.
returnN	if TRUE, returns the vector estimate of N and the matrix a_func instead of the LL
DMs	A list of design matrices if covariates have been included
returnA	If TRUE, will also include the flight pattern densities

calliste-fagard-jenkin/GAI documentation built on July 26, 2022, 11:20 a.m.