DerivedValues: Function to post-process MCMC results of the year-specific...

In benaug/OpenPopSCR: Open Population Spatial Capture-recapture MCMC algorithms

Description

This function derives realized and expected population growth rates and population sizes from the inputted MCMC chains.

Usage

DerivedValues(N, gamma, phi, psi, M, extrap = 0)

Arguments

N	matrix containing the posteriors for abundance
gamma	matrix or vector containing the posteriors for gamma(s)
phi	matrix or vector containing the posteriors for phi(s)
psi	vector containing the posterior for psi
M	an integer indicating the i dimension of the augmented data
extrap	an optional integer indicating how many primary periods to extrapolate beyond the observed primary periods for EN. These are abundance projections from the population growth model

Value

a list containing realized and expected population growth rates and population sizes,

Author(s)

Ben Augustine

Examples

## Not run: 
#Run a model
t=3
N=50
p0=0.5
lam0=-log(1-p0)
sigma=0.750
phi=0.7
gamma=0.3
buff=3
X=list(expand.grid(4:9,4:9),expand.grid(4:9,4:9),expand.grid(4:9,4:9)) #Note we need 3 trap objects stuffed into the trap list
K=c(10,10,10) #and 3 numbers of occasions within primary period
M=225
data=simOpenSCR(N=N,phi=phi,gamma=gamma,lam0=lam0,sigma=sigma,K=K,X=X,t=t,M=M,buff=buff,obstype="bernoulli")
inits=list(lam0=lam0,sigma=sigma,gamma=gamma,phi=phi,psi=N[1]/M)
niter=1000
nburn=0
nthin=1
proppars=list(lam0=0.025,sigma=0.025,gamma=0.1,phi=0.1,s1x=0.2,s1y=0.2,propz=c(30,30)) #Need 1 more propz
out=mcmc.OpenSCR(data,niter=niter,nburn=nburn, nthin=nthin, M =M, inits=inits,proppars=proppars,Rcpp=TRUE)
DV=DerivedValues(out$out[,5:7],out$out[,3],out$out[,4],out$out[,8],M)
str(DV)
library(coda)
plot(mcmc(DV$EN))
plot(mcmc(DV$lambda))
plot(mcmc(DV$Elambda))
#should discard burnin

## End(Not run)

benaug/OpenPopSCR documentation built on Feb. 3, 2022, 10:04 a.m.