multimark (version 2.1.6)

getprobsCJS: 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")

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 (\(k=1,\ldots,T-1\)).

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.

Author

Brett T. McClintock

See Also

multimarkCJS

Examples

# \donttest{
# 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)# }