Question

我使用dirlichet分布在JAGS中拟合多变量模型。我有3种比例丰度的矩阵y。

#generate 3 columns of species proprotional abundance data
y    <- matrix(ncol = 3, nrow = 100)
y[,] <- abs(rnorm(length(y)))
for(i in 1:nrow(y)){
  y[i,] <- y[i,] / sum(y[i,])
}

我有一个预测值的矩阵x，其中第一个是截距。

#generate 2 columns of predictors and an intercept
x <- matrix(ncol = 2, nrow = 100)
x[,] <- rnorm(length(x), mean = 20, sd = 4)
x <- cbind(rep(1,nrow(x)),x)

我指定了多变量jags模型jags.model：

jags.model = "
model {
    #setup parameter priors for each species * predictor combination.
    for(j in 1:N.spp){
      for(k in 1:N.preds){
        m[k,j] ~ dgamma(1.0E-3, 1.0E-3)
      }
    }

    #go ahead and fit means of species abundances as a linear combination of predictor and parameters.
    for(i in 1:N){
        for(j in 1:N.spp){
             log(a0[i,j]) <- m[,j] * x[i,]
           }
    y[i,1:N.spp] ~ ddirch(a0[i,1:N.spp]) 
    }

} #close model loop.
"

我设置了JAGS数据对象jags.data：

jags.data <- list(y = as.matrix(y), x = as.matrix(x),
                  N.spp = ncol(y), N.preds = ncol(x), N = nrow(y))

我使用R。

中的runjags包来适应JAGS模型

jags.out <- runjags::run.jags(jags.model,
                              data=jags.data,
                              adapt = 100,
                              burnin = 200,
                              sample = 400,
                              n.chains=3,
                              monitor=c('m'))

我收到以下错误：

Error: The following error occured when compiling and adapting the model using rjags:
 Error in rjags::jags.model(model, data = dataenv, n.chains = length(runjags.object$end.state),  : 
  RUNTIME ERROR:
Invalid vector argument to exp

我在这里做错了什么？作为参考，通过预测器组合拼出每个参数仍然很合适：

jags.model = "
model {
  #setup parameter priors for each species * predictor combination.
    for(j in 1:N.spp){
      for(k in 1:N.preds){
        m[k,j] ~ dgamma(1.0E-3, 1.0E-3)
      }
    }

  #go ahead and fit means of species abundances as a linear combination of predictor and parameters.
  for(i in 1:N){
    for(j in 1:N.spp){
      log(a0[i,j]) <- m[1,j] * x[i,1] + m[2,j] * x[i,2] + m[3,j] * x[i,3]
    }
    y[i,1:N.spp] ~ ddirch(a0[i,1:N.spp]) 
  }

} #close model loop.
"

Answer 1

此问题的解决方案是在JAGS中采用点积或内积。改变这一行：

log(a0[i,j]) <- m[,j] * x[i,]

为：

log(a0[i,j]) <- inprod(m[,j] , x[i,])

一切都应该正常。完整型号如下。

jags.model = "
model {
    #setup parameter priors for each species * predictor combination.
    for(j in 1:N.spp){
      for(k in 1:N.preds){
        m[k,j] ~ dgamma(1.0E-3, 1.0E-3)
      }
    }

    #go ahead and fit means of species abundances as a linear combination of predictor and parameters.
    for(i in 1:N){
        for(j in 1:N.spp){
             log(a0[i,j]) <- inprod(m[,j] , x[i,])
           }
    y[i,1:N.spp] ~ ddirch(a0[i,1:N.spp]) 
    }

} #close model loop.
"

在JAGS中将参数向量乘以独立变量矩阵

1 个答案: