调用OpenBUGS从R

Question

“集合运算符c错误”我试图使用R2OpenBUGS在OpenBUGS中运行微分方程求解器。 我已经在OpenBUGS/Diff/Examples文件夹中使用了指数衰减示例（Example01.odc）。

这个例子的第一部分是模拟，第二部分是推理版本，我尝试应用。两者都在OpenBUGS中直接运行OK。

当我试图与R运行它，我在日志中得到一个错误：

expected the collection operator c error pos 1443 
variable ngrid is not defined 

我认为第二个是从第一跟进。

下面是我已经编写于从R运行：

# example of adjusting a differential equation using OpenBUGS 
library(R2OpenBUGS) 
library(coda) 
workingdir <- "M:/data/R/OpenBUGSDiff" 
setwd(workingdir) 
# time points 
tgrid <- c(0.00000, 0.20000, 0.40000, 0.60000, 0.80000, 
     1.00000, 1.20000, 1.40000, 1.60000, 1.80000, 
     2.00000, 2.20000, 2.40000, 2.60000, 2.80000, 
     3.00000, 3.20000, 3.40000, 3.60000, 3.80000, 
     4.00000, 4.20000, 4.40000, 4.60000, 4.80000, 
     5.00000, 5.20000, 5.40000, 5.60000, 5.80000, 
     6.00000, 6.20000, 6.40000, 6.60000, 6.80000, 
     7.00000, 7.20000, 7.40000, 7.60000, 7.80000, 
     8.00000, 8.20000, 8.40000, 8.60000, 8.80000, 
     9.00000, 9.20000, 9.40000, 9.60000, 9.80000, 
     10.00000) 
obs <- c( 0.7887,1.241,0.7051,0.7388,0.3903, 
    0.2632,0.1174,0.549,-0.1767,0.02938, 
    0.154,0.1465,0.07878,-0.5569,0.01293, 
    0.2905,-0.2665,-0.3881,0.02517,-0.138, 
    0.4004,0.2859,-0.1217,0.3961,0.3813, 
    0.1846,-0.3581,0.3293,0.04089,0.01972, 
    0.3203,0.5294,-0.1389,-0.3732,0.1341, 
    -0.02432,0.2261,-0.3612,0.3131,-0.258, 
    0.02948,-0.0208,0.1066,0.3796,-0.2645, 
    0.1035,0.1001,-0.2415,0.06739,-0.1554, 
    -0.2388) 
# inference model 
Modele <- function() 
{ 
    solution[1:ngrid, 1] <- 
    ode(init[1], 
     tgrid[1:ngrid], 
     D(C[1], t), 
     origin, 
     tol) 
    D(C[1], t) <- -lambda * C[1] 
    log.lambda ~ dnorm(0.0, tau.lambda); 
    lambda <- exp(log.lambda) 
    for (i in 1:ngrid) 
    { 
    obs[i] ~ dnorm(solution[i, 1], tau) 
    } 
    tau ~ dgamma(a, b) 
} 
write.model(Modele,"Diff.txt") 
# data definition 
origin = 0.0 
tol = 1.0E-3 
ngrid = 51 
init = c(1.0) 
a = 0.001 
b = 0.001 
tau.lambda = 0.01 
data <- list(obs=obs, 
      tgrid=tgrid, 
      origin=origin, 
      tol=tol, 
      ngrid=ngrid, 
      init=init, 
      a=a, 
      b=b, 
      tau.lambda=tau.lambda) 
inits <- function(){ 
    list(log.lambda = 1.0,tau = 0.01) 
} 
diff.inf <- bugs(data,inits,model.file = "Diff.txt", 
       parameters = c("lambda","tau"), 
       n.chains = 1, n.iter = 3000,n.burnin=500,n.thin=10, 
       working.directory=workingdir, 
       debug = TRUE, 
       codaPkg=T) 

这里是从BUGS完整的错误消息：

model is syntactically correct 
expected the collection operator c error pos 1443 
variable ngrid is not defined 
model must have been compiled but not updated to be able to change RN generator 
BugsCmds:NoCompileInits 
model must be compiled before generating initial values 
model must be initialized before updating 
model must be initialized before monitors used 
model must be initialized before monitors used 
model must be initialized before monitors used 
model must be initialized before DIC can be monitored 
model must be initialized before updating 
model must be initialized before monitors used 
DIC monitor not set 

我试图取代“C [] “在模型中”obs“，因为我没有看到”C“的定义在哪里，但是这并没有改变任何东西。

我在科学数字符号中检查了“e”而不是“E”，这在其他地方被建议在BUGS中创建“可变的未定义”错误，但这似乎不成问题。

任何想法，欢迎，或任何其他代码演示了如何提前

谢谢使用“解决方案”或“颂”由内R.

奥利弗

Answer 1

有一个BUGS错误与init节点相关。在上面的模型中，您有一个与其相关的索引（init[1]），但在数据中，您只能提供一个值init = c(1.0)。我认为BUGS在这里与索引相混淆（即它期望数据中有两个或多个初始值，你只提供一个）。当您在模型中将init[1]替换为init时，问题消失。

#BUGS model 
model{ 
    solution[1:ngrid, 1] <- ode(init, tgrid[1:ngrid], D(C[1], t), origin,  tol) 
    D(C[1], t) <- -lambda * C[1] 
    log.lambda ~ dnorm(0.0, tau.lambda); 
    lambda <- exp(log.lambda) 
    for (i in 1:ngrid) { 
    obs[i] ~ dnorm(solution[i, 1], tau) 
    } 
    tau ~ dgamma(a, b) 
} 

#data 
list(obs = c(0.7887, 1.241, 0.7051, 0.7388, 0.3903, 0.2632, 0.1174, 0.549, -0.1767, 0.02938, 0.154, 0.1465, 0.07878, -0.5569, 0.01293, 0.2905, -0.2665, -0.3881, 0.02517, 0.138, 0.4004, 0.2859, -0.1217, 0.3961, 0.3813, 0.1846, -0.3581, 0.3293, 0.04089, 0.01972, 0.3203, 0.5294, -0.1389, -0.3732, 0.1341, -0.02432, 0.2261, -0.3612, 0.3131, -0.258, 0.02948, -0.0208, 0.1066, 0.3796, -0.2645, 0.1035, 0.1001, -0.2415, 0.06739, -0.1554, -0.2388), 
tgrid = c(0, 0.2, 0.4, 0.6, 0.8, 1, 1.2, 1.4, 1.6, 1.8, 2, 2.2, 2.4, 2.6, 2.8, 3, 3.2, 3.4, 3.6, 3.8, 4, 4.2, 4.4, 4.6, 4.8, 5, 5.2, 5.4, 5.6, 5.8, 6, 6.2, 6.4, 6.6, 6.8, 7, 7.2, 7.4, 7.6, 7.8, 8, 8.2, 8.4, 8.6, 8.8, 9, 9.2, 9.4, 9.6, 9.8, 10), 
origin = 0, tol = 0.001, ngrid = 51, init = 1, a = 0.001, b = 0.001, tau.lambda = 0.01)) 

#inits 
list(log.lambda = 1.0,tau = 0.01) 

如果更换上面的前代车型的模型（Modele）一切都应该来自R平稳运行。

一般问题：我发现直接使用OpenBUGS（使用上面的脚本和GUI编译，加载数据和inits）比通过R2OpenBUGS更容易去除bug。