js.lnl {marked}

Likelihood function for Jolly-Seber model using Schwarz-Arnason POPAN formulation

Description

For a given set of parameters and data, it computes -2*log Likelihood value but does not include data factorials. Factorials for unmarked are not needed but are included in final result by js so the result matches output from MARK for the POPAN model.

Usage

js.lnl(par, model_data, debug = FALSE, nobstot, jsenv)

Arguments

par

vector of parameter values

model_data

a list that contains: 1)imat-list of vectors and matrices constructed by process.ch from the capture history data, 2)Phi.dm design matrix for Phi constructed by create.dm, 3)p.dm design matrix for p constructed by create.dm, 4)pent.dm design matrix for probability of entry constructed by create.dm, 5) N.dm design matrix for estimates of number of animals not caught from super-population constructed by create.dm, 6)Phi.fixed matrix with 3 columns: ch number(i), occasion number(j), fixed value(f) to fix phi(i,j)=f, 7) p.fixed matrix with 3 columns: ch number(i), occasion number(j), 8) pent.fixed matrix with 3 columns: ch number(i), occasion number(j), fixed value(f) to fix pent(i,j)=f, and 9) time.intervals intervals of time between occasions if not all 1 fixed value(f) to fix p(i,j)=f

debug

if TRUE will printout values of par and function value

nobstot

number of unique caught at least once by group if applicable

jsenv

environment for js to update iteration counter

Details

This functions uses cjs.lnl and then supplements with the remaining calculations to compute the likelihood for the POPAN formulation (Arnason and Schwarz 1996) of the Jolly-Seber model.

Value

-log likelihood value, excluding data (ui) factorials which are added in js after optimization to match MARK

Author(s)

Jeff Laake

References

Schwarz, C. J., and A. N. Arnason. 1996. A general methodology for the analysis of capture-recapture experiments in open populations. Biometrics 52:860-873.