LLdd: loglikelihood for model

In jayverhoef/MCMCharp: A Quick and Dirty Bayesian Leslie Matrix Model of Norway HarpEast Data

Description

evaluates to the loglikelihood for MCMC sampling

Usage

LLdd(
  N_pup1,
  N_adu1,
  delta,
  phi,
  kappa1,
  rho,
  pdelta_mu,
  pdelta_sd,
  pphi_mu,
  pphi_sd,
  pkappa_mu,
  pkappa_sd,
  prho_mu,
  prho_sd,
  pN_pup1_mu,
  pN_pup1_sd,
  pN_adu1_mu,
  pN_adu1_sd,
  pp,
  H_adu,
  H_pup,
  nyrs
)

Arguments

N_pup1	population value for pups in first year
N_adu1	population value for adults in first year
delta	Leslie matrix parameter for adult survival
phi	Leslie matrix parameter for adult fecundity (both sexes, until survey time)
kappa1	Leslie matrix parameter for pup survival after surveys
rho	parameter for density dependent decay in fecundity
pdelta_mu	mean of normal distribution for prior for logit(delta)
pdelta_sd	standard deviation of normal distribution for prior for logit(delta)
pphi_mu	mean of normal distribution for prior for logit(phi)
pphi_sd	standard deviation of normal distribution for prior for logit(phi)
pkappa_mu	mean of normal distribution for prior for logit(kappa)
pkappa_sd	standard deviation of normal distribution for prior for logit(kappa)
prho_mu	mean of normal distribution for prior for log(rho)
prho_sd	standard deviation of normal distribution for prior for log(rho)
pN_pup1_mu	mean of normal distribution for prior for N_pup1
pN_pup1_sd	standard devitation of normal distribution for prior for N_pup1
pN_adu1_mu	mean of normal distribution for prior for N_adu1
pN_adu1_sd	standard devitation of normal distribution for prior for N_adu1
pp	data set with pup production
H_adu	vector of adult harvest for each year
H_pup	vector of pup harvest for each year
nyrs	number of years (one more than length of harvest vectors)

Value

the loglikelihood

Author(s)

Jay Ver Hoef

jayverhoef/MCMCharp documentation built on Jan. 1, 2021, 4:30 a.m.