Question

我正在尝试使用R2OpenBUGS在OpenBUGS中运行微分方程求解器。我在OpenBUGS / Diff / Examples文件夹中使用指数衰减示例（Example01.odc）尝试过这个。

此示例的第一部分是模拟，第二部分是推理版本，我尝试应用。两者都在OpenBUGS中直接运行。

当我尝试从R运行它时，我在日志中收到错误：

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

我认为第二个是第一个跟进。

以下是我编写的从R运行它的代码：

# 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)

以下是来自BUGS的完整错误消息：

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

我试图用“obs”替换模型中的“C []”，因为我没有看到“C”的定义，但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”，其他地方已经建议在BUGS中创建“变量未定义”错误，但这似乎不是问题。

欢迎任何想法，或任何其他代码，以显示如何使用R中的“解决方案”或“颂歌”。

提前致谢

奥利弗

Answer 1

与init节点有关的BUGS错误。在上面的模型中，您有一个与之关联的索引（init[1]），但在数据中，您只提供一个值init = c(1.0)。我认为BUGS在这里与索引混淆（即它期望数据中有两个或更多init值，你只提供一个）。当您在模型中将init[1]替换为init时，问题就会消失。

#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)

如果您将上述型号替换为之前的型号（Modele），则所有内容都应顺利从R运行。

一般要点：我发现OpenBUGS直接（使用上面的脚本和GUI编译，加载数据和内部）比通过R2OpenBUGS更容易去除bug。

从R调用OpenBUGS时出现“收集运算符c错误”

1 个答案: