Hi, I'm currently working on the below codes however whenever I run it in
openbugs it gives an error message saying: unknown type of logical function
error pos 76. Any help would be appreciated.
## bugs code
library(R2OpenBUGS)
sink("C:/Users/CCF/Documents/Suzie Work/PTY Project/Waterhole
Correction/ungulate.txt")
cat("
model{
# hyperparameters
# habitat effects for each functional group
g <- length(table(G))
for(i in 1:g){ # number of functional group
for(j in 1:3){ # number of habitat type
mu.h[i,j] ~ dnorm(0,0.0001) I(-5,5)
sigma.h[i,j] ~ dunif(0,5)
tau.h[i,j] <- 1/(sigma.h[i,j]*sigma.h[i,j])
}
}
# detectability
mu.r ~ dnorm(0,0.0001) I(-5,5)
sigma.r ~ dunif(0,5)
tau.r <- 1/(sigma.r*sigma.r)
psi ~ dunif(0,1) # inclusion rate that generates wi
# proportion of number of species among groups
for(i in 1:g){
prop[i] ~ dgamma(1,1)
prob[i] <- prop[i]/sum(prop[])
}
for(i in 1:(S+m)){
r[i] ~ dnorm(mu.r,tau.r) I(-5,5) # generating parameters
related to
detectability
p[i] <- 1/(1+exp(-(r[i]))) # individual-level detection
probability
w[i] ~ dbern(psi) # indicator variable
whether each species is exposed
to sampling or not
G[i] ~ dcat(prob[1:g]) # group identity
for(h in 1:3){ # habitat effects
habitat.eff[i,h] ~ dnorm(mu.h[G[i],h],tau.h[G[i],h]) I(-5,5)
}
for(j in 1:20){ # fitting process
# ecological process model
lambda[i,j] <- exp(habitat.eff[i,habitat[j]])
Z[i,j] ~ dpois(lambda[i,j]) # latent abundance of each species at
each site
at each visit
A[i,j] <- Z[i,j]*w[i] # latent abundance only for species
exposed to
sampling
for(v in 1:7){
# detection process model
AY[i,j,v] ~ dbin(p[i],A[i,j])
}
}
# group identity (indicator variable)
G1[i] <- equals(G[i],1)
G2[i] <- equals(G[i],2)
}
for(i in 1:(S+m)){
for(j in 1:20){
A1[i,j] <- A[i,j]*G1[i]
A2[i,j] <- A[i,j]*G2[i]
O[i,j] <- step(A[i,j]-1) # latent occupancy of each
species for each site
O1[i,j] <- O[i,j]*G1[i]
O2[i,j] <- O[i,j]*G2[i]
}
}
for(j in 1:20){
AB0[j] <- sum(A[,j])
AB1[j] <- sum(A1[,j])
AB2[j] <- sum(A2[,j])
SpR0[j] <- sum(O[,j])
SpR1[j] <- sum(O1[,j])
SpR2[j] <- sum(O2[,j])
}
for(i in 1:3){
for(j in 1:7){
HabAB0[i,j] <- AB0[hab[i,j]]
HabAB1[i,j] <- AB1[hab[i,j]]
HabAB2[i,j] <- AB2[hab[i,j]]
HabSpR0[i,j] <- SpR0[hab[i,j]]
HabSpR1[i,j] <- SpR1[hab[i,j]]
HabSpR2[i,j] <- SpR2[hab[i,j]]
}
HAB0[i] <- mean(HabAB0[i,])
HAB1[i] <- mean(HabAB1[i,])
HAB2[i] <- mean(HabAB2[i,])
HSpR0[i] <- mean(HabSpR0[i,])
HSpR1[i] <- mean(HabSpR1[i,])
HSpR2[i] <- mean(HabSpR2[i,])
}
R <- sum(w[1:(S+m)]) # estimating unknown number of species that occupy any
sites
}
",fill=TRUE)
sink()
data <- list("m","S",
"habitat",
"G","g",
# "date",
"hab",
"AY")
g <- length(table(G))
inits <- function()list(
mu.h=matrix(rnorm(6),nrow=2),sigma.h=matrix(runif(6),nrow=2),
mu.r=rnorm(1),sigma.r=runif(1),
r=rnorm(S+m),
prop=runif(n=g,min=0,max=7),
Z=array(rpois(n=(S+m)*20,lambda=20),dim=c((S+m),20)),
w=rep(1,(S+m)),psi=runif(1))
parameters <- c(
"mu.h","sigma.h",
"habitat.eff",
"mu.r","sigma.r",
"r",
"R","psi",
"A",
"O",
"HAB0","HAB1","HAB2",
"HSpR0","HSpR1","HSpR2"
)
out <- bugs (data, inits, parameters,
model.file="C:/Users/CCF/Documents/Suzie Work/PTY Project/Waterhole
Correction/ungulate.txt",
OpenBUGS.pgm="C:/Users/CCF/Desktop/OpenBUGS/OpenBUGS321/OpenBUGS.exe",
n.thin=10, n.burnin=100, n.chains=3,n.iter=1000, debug=TRUE)
--
View this message in context:
http://r.789695.n4.nabble.com/Help-with-R2-OpenBUGs-tp4636412.html
Sent from the R help mailing list archive at Nabble.com.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
