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Zipkin al2010.MultiSpOccurrModelEvaluatEffectConservManagActions s1

artigo cientifico

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Diogo André Alagador
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13 views3 pages

Zipkin al2010.MultiSpOccurrModelEvaluatEffectConservManagActions s1

artigo cientifico

Uploaded by

Diogo André Alagador
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Appendix A.

Supplementary material
Model code

The model code below is written for program R and uses the R2WinBUGS package to run
WinBUGS.

#The detection/non-detection data is defined in a three dimensional


#array X where the first dimension, j, is the point; the second
#dimension, k, is the rep; and the last dimension, i, is the species.
#In addition, all zero encounter histories have been added to the
#array X as part of the data augmentation to account for additional
#species (beyond the n observed species as in Royle et al. 2007 – full
#reference in main text).

#n is the number of observed species


#nzeroes is the number of all-zero encounter histories that has been
#added to the data X
#J is the number of sampled points
#K is a vector of length J indicating the number of reps at each
#point j

#Define the necessary arguments to run the bugs() command

#Load all the data: detection array and covariate information


sp.data = list(n=n, nzeroes=nzeroes, J=J, K=K, X=X, date=date,
date2=date2, sunrise=sunrise, ufc=ufc, ba=ba,
ufc2=ufc2, ba2=ba2, Ind=Ind, ground=ground, mid=mid)

#Specify the parameters to be monitored


sp.params = list('u.cato', 'u.fcw', 'v.cato', 'v.fcw', 'omega',
'a1', 'a2', 'a3', 'a4', 'b1', 'b2', 'b3', 'Nsite', 'N',
'Nground', 'Nmid')

#Specify the initial values


sp.inits = function() {
omegaGuess = runif(1, n/(n+nzeroes), 1)
psi.meanGuess = runif(1, .25,1)
list(omega=omegaGuess,w=c(rep(1, n), rbinom(nzeroes, size=1,
prob=omegaGuess)),
u.cato=rnorm(n+nzeroes), v.cato=rnorm(n+nzeroes),
u.fcw=rnorm(n+nzeroes), v.fcw=rnorm(n+nzeroes),
Z = matrix(rbinom((n+nzeroes)*nsites, size=1,
prob=psi.meanGuess), nrow=nsites, ncol=(n+nzeroes)),
a1=rnorm(n+nzeroes), a2=rnorm(n+nzeroes),
a3=rnorm(n+nzeroes), a4=rnorm(n+nzeroes),
b1=rnorm(n+nzeroes), b2=rnorm(n+nzeroes),
b3=rnorm(n+nzeroes)
)
}

1
#Write the model code to a text file called “deerbrowse.txt”
cat("
model{

#Define prior distributions for community-level model parameters


omega ~ dunif(0,1)

cato.mean ~ dunif(0,1)
mu.ucato <- log(cato.mean) - log(1-cato.mean)

fcw.mean ~ dunif(0,1)
mu.ufcw <- log(fcw.mean) - log(1-fcw.mean)

cato2.mean ~ dunif(0,1)
mu.vcato <- log(cato2.mean) - log(1-cato2.mean)

fcw2.mean ~ dunif(0,1)
mu.vfcw <- log(fcw2.mean) - log(1-fcw2.mean)

mua1 ~ dnorm(0, 0.001)


mua2 ~ dnorm(0, 0.001)
mua3 ~ dnorm(0, 0.001)
mua4 ~ dnorm(0, 0.001)
mub1 ~ dnorm(0, 0.001)
mub2 ~ dnorm(0, 0.001)
mub3 ~ dnorm(0, 0.001)

tau.ucato ~ dgamma(0.1,0.1)
tau.ufcw ~ dgamma(0.1,0.1)
tau.vcato ~ dgamma(0.1,0.1)
tau.vfcw ~ dgamma(0.1,0.1)
tau.a1 ~ dgamma(0.1,0.1)
tau.a2 ~ dgamma(0.1,0.1)
tau.a3 ~ dgamma(0.1,0.1)
tau.a4 ~ dgamma(0.1,0.1)
tau.b1 ~ dgamma(0.1,0.1)
tau.b2 ~ dgamma(0.1,0.1)
tau.b3 ~ dgamma(0.1,0.1)

for (i in 1:(n+nzeroes)) {

#Specify priors for species i from the community level prior


#distributions
w[i] ~ dbern(omega)
u.cato[i] ~ dnorm(mu.ucato, tau.ucato)
u.fcw[i] ~ dnorm(mu.ufws, tau.ufws)
v.cato[i] ~ dnorm(mu.vcato, tau.cato)
v.fcw[i] ~ dnorm(mu.vfws, tau.vfws)
a1[i] ~ dnorm(mua1, tau.a1)
a2[i] ~ dnorm(mua2, tau.a2)
a3[i] ~ dnorm(mua3, tau.a3)
a4[i] ~ dnorm(mua4, tau.a4)

2
b1[i] ~ dnorm(mub1, tau.b1)
b2[i] ~ dnorm(mub2, tau.b2)
b3[i] ~ dnorm(mub3, tau.b3)

#Create a loop to define the Z matrix (true occurrence for species i


#at point j.
for (j in 1:J) {
logit(psi[j,i]) <- u.cato[i]*(1-Ind[j]) + u.fcw[i]*Ind[j] +
a1[i]*ufc[j] + a2[i]*ufc2[j] + a3[i]*ba[j] + a4[i]*ba2[j]

mu.psi[j,i] <- psi[j,i]*w[i]


Z[j,i] ~ dbern(mu.psi[j,i])

#Create a loop to define detection for species i at point k during


#sampling period k.
for (k in 1:K[j]) {
logit(theta[j,k,i]) <- v.cato[i]*(1-Ind[j]) + v.fcw[i]*Ind[j] +
b1[i]*date[j,k] + b2[i]*date2[j,k] + b3[i]*sunrise[j,k]

mu.theta[j,k,i] <- theta[j,k,i]*Z[j,i]


X[j,k,i] ~ dbern(mu.theta[j,k,i])
} } }

#Sum all species observed (n) and unobserved species (n0) to find the
#total estimated richness
n0 <- sum(w[(n+1):(n+nzeroes)])
N <- n + n0

#Create a loop to determine point level richness for the whole


#community and for subsets or assemblages of interest.
for(j in 1:J){
Nsite[j]<- inprod(Z[j,1:(n+nzeroes)],w[1:(n+nzeroes)])
Nground[j]<- inprod(Z[j,1:n],ground[1:n])
Nmid[j]<- inprod(Z[j,1:n],mid[1:n])
}

#Finish writing the text file.


}
",file="biolcons.txt")

#Load the R2Winbugs library


library(R2WinBUGS)

#Run the model and call the results “fit”


fit = bugs(sp.data, sp.inits, sp.params, "biolcons.txt", debug=TRUE,
n.chains=3, n.iter=30000, n.burnin=20000, n.thin=10)

#See a summary of the parameter estimates


fit$summary

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