DerivedValuesSex: Function to post-process MCMC results for the sex-specific...

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

Description

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

Usage

DerivedValuesSex(Nm, Nf, gamma, phi, psex, psi, M, extrap = 0)

Arguments

Nm	matrix containing the posteriors for the number of males
Nf	matrix containing the posteriors for the number of females
gamma	matrix or vector (if sex-specific) containing the posteriors for gamma(s)
phi	matrix or vector (if sex-specific) containing the posteriors for phi(s)
psex	vector containing the posterior for psex
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, ENm, and ENf. These are abundance projections from the population growth model

Value

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

Author(s)

Ben Augustine

Examples

## Not run: 
#Run a sex-specific model
t=3
N=c(40,40)
p0=c(0.25,0.5)
lam0=-log(1-p0)
sigma=c(0.75,0.5)
phi=c(0.4,0.8)
gamma=c(0.4,0.1)
buff=3
X=list(expand.grid(4:9,4:9),expand.grid(4:9,4:9),expand.grid(4:9,4:9))
K=c(10,10,10)
M=250
pIDsex=0.75
obstype="bernoulli"
ACtype="metamu"
data=simOpenSCRsex(N=N,gamma=gamma,phi=phi,lam0=lam0,sigma=sigma,K=K,X=X,t=t,M=M,buff=buff,
                   ACtype=ACtype,obstype="bernoulli",pIDsex=pIDsex,sigma_t=sigma_t)
inits=list(lam0=lam0,sigma=sigma,gamma=gamma,phi=phi,psi=(sum(N)/M),psex=0.5)
niter=1000
nburn=0
nthin=1
proppars=list(lam0=c(0.075,0.115),sigma=c(0.055,0.045),gamma=c(0.115,0.085),s1x=0.4,s1y=0.4,
sigma_t=c(0.04,0.03),sex=100)
out=mcmc.OpenSCR.sex(data,niter=niter,nburn=nburn, nthin=nthin, M=M, inits=inits,proppars=proppars,
ACtype=ACtype)
DV=DerivedValuesSex(out$out[,12:14],out$out[,15:17],out$out[,5:6],out$out[,7:8],out$out[,18],out$out[,19],M)
str(DV)
library(coda)
plot(mcmc(DV$lambdaM))
plot(mcmc(DV$lambdaF))
#etc.
#should discard burnin

## End(Not run)

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