【发布时间】：2014-04-25 00:58:36
【问题描述】：
我正在使用 OpenBUGS 和 R 包 R2OpenBUGS 研究二项式混合模型。我已经成功地构建了更简单的模型，但是一旦我为不完美的检测添加了另一个级别，我一直收到错误variable X is not defined in model or in data set。我尝试了许多不同的方法，包括更改我的数据结构和将我的数据直接输入 OpenBUGS。我发布此消息是希望其他人有此错误的经验，并且也许知道为什么 OpenBUGS 无法识别变量 X，尽管据我所知它已明确定义。
我也收到了错误 expected the collection operator c error pos 8 - 这不是我之前遇到的错误，但我同样感到困惑。
模型和数据模拟功能均来自 Kery 为生态学家编写的 WinBUGS 简介 (2010)。我会注意，这里的数据集是代替我自己的数据，这是相似的。
我包括构建数据集和模型的功能。抱歉，篇幅较长。
# Simulate data: 200 sites, 3 sampling rounds, 3 factors of the level 'trt',
# and continuous covariate 'X'
data.fn <- function(nsite = 180, nrep = 3, xmin = -1, xmax = 1, alpha.vec = c(0.01,0.2,0.4,1.1,0.01,0.2), beta0 = 1, beta1 = -1, ntrt = 3){
y <- array(dim = c(nsite, nrep)) # Array for counts
X <- sort(runif(n = nsite, min = xmin, max = xmax)) # covariate values, sorted
# Relationship expected abundance - covariate
x2 <- rep(1:ntrt, rep(60, ntrt)) # Indicator for population
trt <- factor(x2, labels = c("CT", "CM", "CC"))
Xmat <- model.matrix(~ trt*X)
lin.pred <- Xmat[,] %*% alpha.vec # Value of lin.predictor
lam <- exp(lin.pred)
# Add Poisson noise: draw N from Poisson(lambda)
N <- rpois(n = nsite, lambda = lam)
table(N) # Distribution of abundances across sites
sum(N > 0) / nsite # Empirical occupancy
totalN <- sum(N) ; totalN
# Observation process
# Relationship detection prob - covariate
p <- plogis(beta0 + beta1 * X)
# Make a 'census' (i.e., go out and count things)
for (i in 1:nrep){
y[,i] <- rbinom(n = nsite, size = N, prob = p)
}
# Return stuff
return(list(nsite = nsite, nrep = nrep, ntrt = ntrt, X = X, alpha.vec = alpha.vec, beta0 = beta0, beta1 = beta1, lam = lam, N = N, totalN = totalN, p = p, y = y, trt = trt))
}
data <- data.fn()
这是模型：
sink("nmix1.txt")
cat("
model {
# Priors
for (i in 1:3){ # 3 treatment levels (factor)
alpha0[i] ~ dnorm(0, 0.01)
alpha1[i] ~ dnorm(0, 0.01)
}
beta0 ~ dnorm(0, 0.01)
beta1 ~ dnorm(0, 0.01)
# Likelihood
for (i in 1:180) { # 180 sites
C[i] ~ dpois(lambda[i])
log(lambda[i]) <- log.lambda[i]
log.lambda[i] <- alpha0[trt[i]] + alpha1[trt[i]]*X[i]
for (j in 1:3){ # each site sampled 3 times
y[i,j] ~ dbin(p[i,j], C[i])
lp[i,j] <- beta0 + beta1*X[i]
p[i,j] <- exp(lp[i,j])/(1+exp(lp[i,j]))
}
}
# Derived quantities
}
",fill=TRUE)
sink()
# Bundle data
trt <- data$trt
y <- data$y
X <- data$X
ntrt <- 3
# Standardise covariates
s.X <- (X - mean(X))/sd(X)
win.data <- list(C = y, trt = as.numeric(trt), X = s.X)
# Inits function
inits <- function(){ list(alpha0 = rnorm(ntrt, 0, 2),
alpha1 = rnorm(ntrt, 0, 2),
beta0 = rnorm(1,0,2), beta1 = rnorm(1,0,2))}
# Parameters to estimate
parameters <- c("alpha0", "alpha1", "beta0", "beta1")
# MCMC settings
ni <- 1200
nb <- 200
nt <- 2
nc <- 3
# Start Markov chains
out <- bugs(data = win.data, inits, parameters, "nmix1.txt", n.thin=nt,
n.chains=nc, n.burnin=nb, n.iter=ni, debug = TRUE)
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标签： r bayesian winbugs r2winbugs