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AYNA_IPM_mean_projection_no_skip.jags
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AYNA_IPM_mean_projection_no_skip.jags
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model {
#-------------------------------------------------
# integrated population model for the Gough AYNA population
# - age structured model with 6 age classes
# - adult survival based on CMR ringing data
# - pre breeding census, female-based assuming equal sex ratio & survival
# - productivity based on Area 1 nest monitoring data
# - simplified population process with informed prior for adults skipping breeding and uninformed immatures recruiting
# - FOUR future scenarios to project population growth after eradication, bycatch mitigation or no management
# -------------------------------------------------
#-------------------------------------------------
# 1. PRIORS FOR ALL DATA SETS
#-------------------------------------------------
# -------------------------------------------------
# 1.1. Priors and constraints FOR FECUNDITY
# -------------------------------------------------
for (t in 1:T){
ann.fec[t] ~ dunif(0,1) # Priors on fecundity can range from 0-1 chicks per pair (constrained based on our data)
imm.rec[t] ~ dunif(0,1) ## RECRUITMENT PROBABILITY COULD SET MORE INFORMATIVE PRIOR HERE
#skip.prob[t] ~ dunif(0,1) ## PRIOR FOR ADULT BREEDER SKIPPING PROBABILITY from Cuthbert paper that reported breeding propensity of 0.66
} #t
# -------------------------------------------------
# 1.2. Priors and constraints FOR POPULATION COUNTS
# -------------------------------------------------
for (s in 1:n.sites){ ### start loop over every study area
N.est[1,s] ~ dunif(0,200) ## draw random value from a uniform distribution between 0 and 200 for initial population size
mean.lambda[s] ~ dunif(0,10) #Prior for mean growth rate
sigma.proc[s] ~ dunif(0,10) #Prior for SD of state process (annual variation in pop size)
sigma2.proc[s]<-pow(sigma.proc[s],2)
tau.proc[s]<-pow(sigma.proc[s],-2)
sigma.obs[s] ~ dunif(0,100) #Prior for SD of observation process (variation in detectability)
sigma2.obs[s]<-pow(sigma.obs[s],2)
tau.obs[s]<-pow(sigma.obs[s],-2)
}
# -------------------------------------------------
# 1.3. Priors and constraints FOR SURVIVAL
# -------------------------------------------------
### RECAPTURE PROBABILITY
mean.p ~ dunif(0, 1) # Prior for mean recapture
logit.p <- log(mean.p / (1-mean.p)) # Logit transformation
for (t in 1:T){
logit(p[t]) <- logit.p + capt.raneff[t]
capt.raneff[t] ~ dnorm(0, tau.capt)
}
### SURVIVAL PROBABILITY
for (i in 1:nind){
for (t in f[i]:(T-1)){
logit(phi[i,t]) <- mu[AGEMAT[i,t]] + surv.raneff[t] + bycatch*longline[t]
} #t
} #i
## AGE-SPECIFIC SURVIVAL
for (age in 1:2){
beta[age] ~ dunif(0, 1) # Priors for age-specific survival
mu[age] <- log(beta[age] / (1-beta[age])) # Logit transformation
}
## RANDOM TIME EFFECT ON SURVIVAL
for (t in 1:(T-1)){
surv.raneff[t] ~ dnorm(0, tau.surv)
}
### PRIORS FOR RANDOM EFFECTS
sigma.surv ~ dunif(0, 10) # Prior for standard deviation of survival
tau.surv <- pow(sigma.surv, -2)
sigma.capt ~ dunif(0, 10) # Prior for standard deviation of capture
tau.capt <- pow(sigma.capt, -2)
### PRIOR FOR BYCATCH EFFECTS
bycatch ~ dnorm(0,tau.byc)
sigma.byc ~ dunif(0, 10) # Prior for standard deviation of capture
tau.byc <- pow(sigma.byc, -2)
#-------------------------------------------------
# 2. LIKELIHOODS AND ECOLOGICAL STATE MODEL
#-------------------------------------------------
# -------------------------------------------------
# 2.1. System process: female based matrix model
# -------------------------------------------------
for (tt in 2:T){
## THE PRE-BREEDING YEARS ##
nestlings[tt] <- ann.fec[tt] * 0.5 * Ntot.breed[tt] ### number of locally produced FEMALE chicks
JUV[tt] ~ dpois(nestlings[tt]) ### need a discrete number otherwise dbin will fail, dpois must be >0
N1[tt] ~ dbin(ann.surv[1,tt-1], round(JUV[tt-1])) ### number of 1-year old survivors
N2[tt] ~ dbin(ann.surv[1,tt-1], round(N1[tt-1])) ### number of 2-year old survivors
N3[tt] ~ dbin(ann.surv[1,tt-1], round(N2[tt-1])) ### number of 3-year old survivors
N4[tt] ~ dbin(ann.surv[1,tt-1], round(N3[tt-1])) ### number of 4-year old survivors
N5[tt] ~ dbin(ann.surv[1,tt-1], round(N4[tt-1])) ### number of 5-year old survivors
## THE POTENTIAL RECRUITING YEARS ##
N6[tt] ~ dbin(ann.surv[2,tt-1], round(N5[tt-1])) ### number of 6-year old survivors that are ready for recruitment - using adult survival
N.notrecruited[tt] ~ dbin(ann.surv[2,tt-1], round(max(10,non.recruits[tt-1]))) ### number of not-yet-recruited birds surviving from previous year
non.recruits[tt]<-(N6[tt]+N.notrecruited[tt])-ann.recruits[tt] ## number of birds that do not recruit is the sum of all available minus the ones that do recruit
## THE BREEDING YEARS ##
Ntot.breed[tt] ~ dpois(pop.size[tt]) ### the annual number of breeding birds is the estimate from the count SSM
ann.recruits[tt] ~ dbin(imm.rec[tt],round(N6[tt]+N.notrecruited[tt])) ### Ntot.breed[tt]-Nold.breed[tt]+1)) ### this total number comprises a bunch of new recruits, which is the number of total breeders that are not old breeders
Nold.breed[tt]<- N.pot.breed[tt]-N.non.breed[tt] ### number of old breeders is survivors from previous year minus those that skip a year of breeding
N.pot.breed[tt] ~ dbin(ann.surv[2,tt-1], round(sum(Ntot.breed[tt-1],N.non.breed[tt-1]))) ### number of potential old breeders is the number of survivors from previous year breeders and nonbreeders
N.non.breed[tt] ~ dbin((1-p[tt]), round(N.pot.breed[tt])) ### number of old nonbreeders (birds that have bred before and skip breeding)
} # tt
### INITIAL VALUES FOR COMPONENTS FOR YEAR 1 - based on stable stage distribution from previous model
JUV[1]<-round(Ntot.breed[1]*0.5*ann.fec[1])
N1[1]<-round(Ntot.breed[1]*0.17574058)
N2[1]<-round(Ntot.breed[1]*0.11926872)
N3[1]<-round(Ntot.breed[1]*0.10201077)
N4[1]<-round(Ntot.breed[1]*0.08725001)
N5[1]<-round(Ntot.breed[1]*0.07462511)
non.recruits[1]<-round(Ntot.breed[1]*0.3147774)
Ntot.breed[1]<-sum(y.count[1,])
N.non.breed[1]<- round(Ntot.breed[1]*0.12632740)
# -------------------------------------------------
# 2.2. Observation process for population counts: state-space model of annual counts
# -------------------------------------------------
for (s in 1:n.sites){ ### start loop over every study area
## State process for entire time series
for (t in 1:(T-1)){
lambda[t,s] ~ dnorm(mean.lambda[s], tau.proc[s]) # Distribution for random error of growth rate
N.est[t+1,s]<-N.est[t,s]*lambda[t,s] # Linear predictor (population size based on past pop size and change rate)
} # run this loop over nyears
## Observation process
for (t in 1:T){
y.count[t,s] ~ dnorm(N.est[t,s], tau.obs[s]) # Distribution for random error in observed numbers (counts)
} # run this loop over t= nyears
} ## end site loop
# -------------------------------------------------
# 2.3. Likelihood for fecundity: Poisson regression from the number of surveyed broods
# -------------------------------------------------
for (t in 1:(T-1)){
J[t] ~ dpois(rho.fec[t])
rho.fec[t] <- R[t]*ann.fec[t]
} # close loop over every year in which we have fecundity data
# -------------------------------------------------
# 2.4. Likelihood for adult and juvenile survival from CMR
# -------------------------------------------------
# Likelihood
for (i in 1:nind){
# Define latent state at first capture
z[i,f[i]] <- 1
for (t in (f[i]+1):T){
# State process
z[i,t] ~ dbern(mu1[i,t])
mu1[i,t] <- phi[i,t-1] * z[i,t-1]
# Observation process
y[i,t] ~ dbern(mu2[i,t])
mu2[i,t] <- p[t] * z[i,t]
} #t
} #i
#-------------------------------------------------
# 3. DERIVED PARAMETERS FOR OUTPUT REPORTING
#-------------------------------------------------
## DERIVED SURVIVAL PROBABILITIES PER YEAR
for (t in 1:(T-1)){
for (age in 1:2){
logit(ann.surv[age,t]) <- mu[age] + surv.raneff[t]
}
}
## DERIVED POPULATION SIZE PER YEAR
for (t in 1:T){
pop.size[t]<-max(10,sum(N.est[t,1:n.sites])) ## introduced max to prevent this number from being 0 which leads to invalid parent error on Ntot.breed
}
## DERIVED OVERALL POPULATION GROWTH RATE
pop.growth.rate <- mean(lambda[1:(T-1),1:n.sites]) # Arithmetic mean for whole time series
## DERIVED MEAN FECUNDITY
mean.fec <- mean(ann.fec)
mean.rec <- mean(imm.rec)
#sd.fec <- sd(ann.fec)
#tau.fec <- pow(max(sd.fec,0.01),-2)
#-------------------------------------------------
# 4. PROJECTION INTO FUTURE
#-------------------------------------------------
for (tt in (T+1):FUT.YEAR){
## RANDOMLY DRAW DEMOGRAPHIC RATES FROM PREVIOUS YEARS WHILE AVOIDING THAT INDEX BECOMES 0
#FUT[tt] ~ dunif(1.5,15.5) ### CHANGE FROM 1.5 to 15.5 to only sample from last three years when survival was high
#FUT.int[tt]<-round(FUT[tt])
#fut.fec[tt] ~ dnorm(mean.fec,tau.fec) ### CHANGE FROM mean.fec to 0.69 + 0.16 from Caravaggi et al. 2018 for eradication scenario
# -------------------------------------------------
# 4.1. System process for future
# -------------------------------------------------
## THE PRE-BREEDING YEARS ##
nestlings[tt] <- round(mean.fec* 0.5 * Ntot.breed[tt]) ### number of locally produced FEMALE chicks based on average fecundity - to use just one take ann.fec[FUT.int[tt]]
N1[tt] ~ dbin(beta[1], max(1,round(nestlings[tt-1]))) ### number of 1-year old survivors
N2[tt] ~ dbin(beta[1], round(N1[tt-1])) ### number of 2-year old survivors
N3[tt] ~ dbin(beta[1], round(N2[tt-1])) ### number of 3-year old survivors
N4[tt] ~ dbin(beta[1], round(N3[tt-1])) ### number of 4-year old survivors
N5[tt] ~ dbin(beta[1], round(N4[tt-1])) ### number of 5-year old survivors
## THE POTENTIAL RECRUITING YEARS ##
N6[tt] ~ dbin(beta[2], round(N5[tt-1])) ### number of 6-year old survivors that are ready for recruitment - using adult survival
N.notrecruited[tt] ~ dbin(beta[2], round(max(10,non.recruits[tt-1]))) ### number of not-yet-recruited birds surviving from previous year
non.recruits[tt]<-(N6[tt]+N.notrecruited[tt])-ann.recruits[tt] ### number of birds that do not recruit is the sum of all available minus the ones that do recruit
ann.recruits[tt] ~ dbin(mean.rec,round(N6[tt]+N.notrecruited[tt])) ### new recruits
## THE BREEDING YEARS ##
Ntot.breed[tt] <- Nold.breed[tt] + ann.recruits[tt] ### the annual number of breeding birds is the estimate from the count SSM
Nold.breed[tt]<- N.pot.breed[tt]-N.non.breed[tt] ### number of old breeders is survivors from previous year minus those that skip a year of breeding
N.pot.breed[tt] ~ dbin(beta[2], round(sum(Ntot.breed[tt-1],N.non.breed[tt-1]))) ### number of potential old breeders is the number of survivors from previous year breeders and nonbreeders
N.non.breed[tt] ~ dbin((1-mean.p), round(N.pot.breed[tt])) ### number of old nonbreeders (birds that have bred before and skip breeding)
## CALCULATE ANNUAL POP GROWTH RATE ##
fut.lambda[tt-19] <- Ntot.breed[tt]/max(1,Ntot.breed[tt-1]) ### inserted safety to prevent denominator being 0
} # tt
# -------------------------------------------------
# 4.2. DERIVED POPULATION GROWTH RATE FOR FUTURE
# -------------------------------------------------
## DERIVED OVERALL POPULATION GROWTH RATE
future.growth.rate <- mean(fut.lambda[1:10]) # projected ANNUAL growth rate in the future
}