From: <James.Dell_at_csiro.au>

Date: Fri, 4 Jan 2008 11:15:37 +1100

# mixture

YFTCPUE[i] ~ dpois(mu.i[i])

}

R-help_at_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. Received on Fri 04 Jan 2008 - 00:19:11 GMT

Date: Fri, 4 Jan 2008 11:15:37 +1100

Hello R and BUGS users,

I am writing a heirarchical model in R to send to BUGS via R2WinBUGS and
I am finding it difficult to get the model to run. I seem to be having
two problems.

1) I can't seem to send variables classed as factors (Month), is there a
way do this?

2) Checking the Log in WinBUGS I can see that the model is Syntactically
correct, but Bugs is not able to recognise the the initial values for
each of the chains.

I have been following the examples provided in the R vignette for
R2WinBUGS and I am a little stumped on what do do next. Any suggestions
and help will be greatly appreciated.

The Model and the R Code have been using are below. The Error from
WinBUGS is at the end of this mail.

Kind Regards

Jim Dell

Phd Candidate

Quantitative Marine Science

University of Tasmania and CSIRO Marine and Atmospheric Research
ph +62 3 6232 5182

mb +61 429 32 5182

model

{

#Centre variables

mSeaW <- mean(SeaW[])

s_dSeaW <- sd(SeaW[])

#normalise Variables

nSeaWiFS <- mSeaW/s_dSeaW

for(i in 1:N) {

log(lambda[i]) <- delta0 + alpha1 * Month[i] + alpha2 * Lat[i] +
beta1 * (SeaW[i] - nSeaW)

logit(p[i]) <- gamma0

mu[i, 1] <- 0

mu[i, 2] <- lambda[i]

mu.i[i] <- mu[i, index[i]]

index[i] ~ dcat(theta[i, 1:2]) theta[i, 1] <- p[i] theta[i, 2] <- 1 - p[i]

# mixture

YFTCPUE[i] ~ dpois(mu.i[i])

}

# recalculate the original intercept term

Intercept <- delta0 - beta1 * nSeaW

#prior on regression coefficients

beta1 ~ dnorm(0,1.0E-6)

alpha2 ~ dnorm(0,1.0E-6) alpha1 ~ dnorm(0, 1.0E-6) delta0 ~ dnorm(0, 1.0E-6) gamma0 ~ dnorm(0, 1.0E-6)

}

##R Code

library(R2WinBUGS)

library(Rlab)

#sampling functions

#get a subset of the data to use in the modelling process
LearnSamp <- function (dBUGS) # data frame of the variables of interest

{ rnames<- row.names(dBUGS) sampRows <- sample(rnames,900) learnSamp <- subset(dBUGS,rnames%in%sampRows) }

#maybe not needed index.inits <- function () # get data into correct form for R2WinBUGS

d <-LearnSamp(dBUGS)

YFTCPUE <- d$CPUE

Month <- d$Month

Lat <- d$Lat

SeaW <- d$SeaW

N <- nrow(d)

data <- list("N", "YFTCPUE","Lat","SeaW") #,"Month" #Month Taken out so that model runs

#create initial values for the coefficients in the model (this is model
specific)

#construct inits for the three chain

inits1 <- list(gamma0 = 0, delta0 = 0,beta1 = 0, alpha1 = 0, alpha2 = 0,
index = rbern(J,0.5)+1)

inits2 <- list(gamma0 = 0, delta0 = 0,beta1 = 0, alpha1 = 0, alpha2 = 0,
index = rbern(J,0.5)+1)

inits3 <- list(gamma0 = 0, delta0 = 0,beta1 = 0, alpha1 = 0, alpha2 = 0,
index = rbern(J,0.5)+1)

inits <- list(inits1,inits2,inits3)

## these data.frames need to be trimmed so that we can send varibles to WinBUGS

parameters <- c("gamma0", "delta0", "beta1", "alpha1","alpha2", "index")
model <- bugs(data, inits, parameters,

model.file = "C:/Documents and Settings/del125/My Documents/PhD
data/ETBF - BUGS/CodeR2BUGS/MinusMonthSeaWiFS.bug",
codaPkg = FALSE, bugs.directory = "C:/Program Files/WinBUGS14/", debug
**=TRUE)
**
##And the Error Message from WinBUGS

model is syntactically correct

data(C:/Program Files/R/R-2.6.0/data.txt)

made use of undefined node nSeaW

inits(1,C:/Program Files/R/R-2.6.0/inits1.txt)

command #Bugs:inits cannot be executed (is greyed out)

inits(2,C:/Program Files/R/R-2.6.0/inits2.txt)

command #Bugs:inits cannot be executed (is greyed out)

inits(3,C:/Program Files/R/R-2.6.0/inits3.txt)

command #Bugs:inits cannot be executed (is greyed out)

gen.inits()

command #Bugs:gen.inits cannot be executed (is greyed out)

thin.updater(3)

update(334)

command #Bugs:update cannot be executed (is greyed out)

(error continues.....)

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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. Received on Fri 04 Jan 2008 - 00:19:11 GMT

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