cjs.fn: Summarizes detection histories and provides...

In Columbia-Basin-Research-West/cbrATLAS: Active Tag Life Adjusted Survival Modeling

Summarizes detection histories and provides Cormack-Jolly-Seber estimates with or without adjustment of potential tag-failure

Description

CJS.fn summarizes the individual detection histories and estimates seeds for Cormack-Jolly-Seber (CJS) likelhood function. It is based on Skalski et al. (1998). This likelihood is also used to adjust survival for estimated tag life as described in Townsend et al. (2006). If no tag-life data provided, only the unadjusted CJS survival will be returned.

Usage

cjs.fn(detect.in, L.in = NULL, seeds.in = NULL, se.out = F, d = NULL)

Arguments

detect.in	Detection history in wide ATLAS format without rel.group or bin columns
L.in	L.in: Vector of mean probabilities tag is working given detection at each site. If NULL, function will estimate the CJS parameters without tag failure
seeds.in	Optional starting estimates for CJS model parameters Si, pi, li where i is 1:(total number of sites-1)
se.out	(T|F) Should standard error of cjs parameters be estimated. Uses variance matrix based on Hessian from MLE of cjs likelihood
d	proportion of detected tags censored at a location

Value

Returns a two-column matrix with CJS estimates and standard errors (if estimated)

Columbia-Basin-Research-West/cbrATLAS documentation built on April 1, 2022, 1:52 p.m.