getprobsCJS {multimark}

Calculate posterior capture and survival probabilities

Description

This function calculates posterior capture (p) and survival (\phi) probabilities for each sampling occasion from multimarkCJS output.

Usage

getprobsCJS(out, link = "probit")

Arguments

out

List of output returned by multimarkCJS

link

Link function for p and \phi. Must be "probit" or "logit". Note that multimarkCJS is currently implemented for the probit link only.

Value

An object of class mcmc.list containing the following:

p

Posterior samples for capture probability (p[c,t]) for each release cohort (c=1,\ldots,T-1) and sampling occasion (t=2,\ldots,T).

phi

Posterior samples for survival probability (\phi[c,k]) for each release cohort (c=1,\ldots,T-1) and interval (k=1,\ldots,T-1).

Author(s)

Brett T. McClintock

See Also

multimarkCJS

Examples

# This example is excluded from testing to reduce package check time
# Example uses unrealistically low values for nchain, iter, and burnin

#Simulate open population data with temporal variation in survival
noccas <- 5
data <- simdataCJS(noccas=noccas, phibeta=rnorm(noccas-1,1.6,0.1))
 
#Fit open population model with temporal variation in survival
sim.time <- multimarkCJS(data$Enc.Mat,mod.phi=~time)
    
#Calculate capture and survival probabilities for each cohort and time
pphi <- getprobsCJS(sim.time)
summary(pphi)