[英]jags.parallel - Error in get(name, envir = envir) : invalid first argument
When using jags.parallel
, I get the following error: 使用
jags.parallel
,我收到以下错误:
> out <- jags.parallel(win.data, inits, params, "Poisson.OD.t.test.txt",
+ nc, ni, nb, nt);
Error in get(name, envir = envir) : invalid first argument
The same call using jags
function runs OK. 使用
jags
函数的相同调用运行正常。 I have only found one thread on this topic , but there is only one speculative suggestion that does not apply nor work here. 我只在这个主题上找到了一个主题 ,但只有一个推测性的建议不适用也不适用于此。
Reproducible code, taken from Introduction to WinBUGS for ecologists, see chapter 14.1 (slightly modified): 可重复使用的代码,取自生态学家的WinBUGS简介,参见第14.1章 (稍作修改):
set.seed(123)
### 14.1.2. Data generation
n.site <- 10
x <- gl(n = 2, k = n.site, labels = c("grassland", "arable"))
eps <- rnorm(2*n.site, mean = 0, sd = 0.5)# Normal random effect
lambda.OD <- exp(0.69 +(0.92*(as.numeric(x)-1) + eps) )
lambda.Poisson <- exp(0.69 +(0.92*(as.numeric(x)-1)) ) # For comparison
C.OD <- rpois(n = 2*n.site, lambda = lambda.OD)
C.Poisson <- rpois(n = 2*n.site, lambda = lambda.Poisson)
### 14.1.4. Analysis using WinBUGS
# Define model
sink("Poisson.OD.t.test.txt")
cat("
model {
# Priors
alpha ~ dnorm(0,0.001)
beta ~ dnorm(0,0.001)
sigma ~ dunif(0, 10)
tau <- 1 / (sigma * sigma)
maybe_overdisp <- mean(exp_eps[])
# Likelihood
for (i in 1:n) {
C.OD[i] ~ dpois(lambda[i])
log(lambda[i]) <- alpha + beta *x[i] #+ eps[i]
eps[i] ~ dnorm(0, tau)
exp_eps[i] <- exp(eps[i])
}
}
",fill=TRUE)
sink()
# Bundle data
win.data <- list(C.OD = C.OD, x = as.numeric(x)-1, n = length(x))
# Inits function
inits <- function(){ list(alpha=rlnorm(1), beta=rlnorm(1), sigma = rlnorm(1))}
# Parameters to estimate
params <- c("lambda","alpha", "beta", "sigma", "maybe_overdisp")
# MCMC settings
nc <- 3 # Number of chains
ni <- 3000 # Number of draws from posterior per chain
nb <- 1000 # Number of draws to discard as burn-in
nt <- 5 # Thinning rate
require(R2jags)
# THIS WORKS FINE
out <- R2jags::jags(win.data, inits, params, "Poisson.OD.t.test.txt",
nc, ni, nb, nt);
# THIS PRODUCES ERROR
out <- jags.parallel(win.data, inits, params, "Poisson.OD.t.test.txt",
nc, ni, nb, nt);
# THIS ALSO PRODUCES ERROR
out <- do.call(jags.parallel, list(win.data, inits, params, "Poisson.OD.t.test.txt",
nc, ni, nb, nt));
Jags/R had practically two problems with this line: Jags / R几乎有两个问题:
out <- jags.parallel(win.data, inits, params, "Poisson.OD.t.test.txt",
nc, ni, nb, nt);
Both are related to evaluation of function parameters - he is probably not able to resolve parameters which refer to other R variables: 两者都与函数参数的评估有关 - 他可能无法解析引用其他R变量的参数:
1) The win.data
was encoded as variable names as usually for WinBUGS/Jags: 1)
win.data
被编码为变量名,通常用于WinBUGS / Jags:
win.data <- list(C.OD = C.OD, x = as.numeric(x)-1, n = length(x))`
but jags.parallel
issues the error "Error in get(name, envir = envir) : invalid first argument". 但是
jags.parallel
发出错误“get(name,envir = jags.parallel
的错误:第一个参数无效”。 He wants the data in this format: 他想要这种格式的数据:
windata <- list("C.OD", "x", "n")
Why? 为什么? Don't ask me... I discovered this when reading the example of
?jags
. 不要问我......我在阅读“
?jags
的例子时发现了这一点。
2) The arguments nc, ni, nb, nt
in function call are a problem! 2)函数调用中的参数
nc, ni, nb, nt
是个问题! If I put constants, it is OK, but references to variables are unacceptable for him. 如果我把常量,它没关系,但对变量的引用对他来说是不可接受的。 Don't ask me why.
不要问我为什么。 Remedy found at strange jags.parallel error / avoiding lazy evaluation in function call .
在奇怪的jags.parallel错误/避免函数调用中的惰性求值时发现的补救措施。
The complete fix looks like: 完整的修复如下:
out <- do.call(jags.parallel, list(names(win.data), inits, params, "Poisson.OD.t.test.txt",
nc, ni, nb, nt));
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