[英]tryCatch - namespace?
I am quite new to R and I am confused by the correct usage of tryCatch
. 我对R很新,我对
tryCatch
的正确用法感到困惑。 My goal is to make a prediction for a large data set. 我的目标是对大型数据集进行预测。 If the predictions cannot fit into memory, I want to circumvent the problem by splitting my data.
如果预测无法适应内存,我想通过拆分数据来规避问题。
Right now, my code looks roughly as follows: 现在,我的代码大致如下:
tryCatch({
large_vector = predict(model, large_data_frame)
}, error = function(e) { # I ran out of memory
for (i in seq(from = 1, to = dim(large_data_frame)[1], by = 1000)) {
small_vector = predict(model, large_data_frame[i:(i+step-1), ])
save(small_vector, tmpfile)
}
rm(large_data_frame) # free memory
large_vector = NULL
for (i in seq(from = 1, to = dim(large_data_frame)[1], by = 1000)) {
load(tmpfile)
unlink(tmpfile)
large_vector = c(large_vector, small_vector)
}
})
The point is that if no error occurs, large_vector
is filled with my predictions as expected. 关键是如果没有发生错误,
large_vector
会按预期填充我的预测。 If an error occurs, large_vector
seems to exist only in the namespace of the error code - which makes sense because I declared it as a function. 如果发生错误,
large_vector
似乎只存在于错误代码的命名空间中 - 这是有道理的,因为我将其声明为函数。 For the same reason, I get a warning saying that large_data_frame
cannot be removed. 出于同样的原因,我收到一条警告,说无法删除
large_data_frame
。
Unfortunately, this behavior is not what I want. 不幸的是,这种行为不是我想要的。 I would want to assign the variable
large_vector
from within my error function. 我想从我的错误函数中分配变量
large_vector
。 I figured that one possibility is to specify the environment and use assign. 我认为一种可能性是指定环境并使用assign。 Thus, I would use the following statements in my error code:
因此,我会在我的错误代码中使用以下语句:
rm(large_data_frame, envir = parent.env(environment()))
[...]
assign('large_vector', large_vector, parent.env(environment()))
However, this solution seems rather dirty to me. 但是,这个解决方案对我来说似乎很脏。 I wonder whether there is any possibility to achieve my goal with "clean" code?
我想知道是否有可能用“干净”的代码实现我的目标?
[EDIT] There seems to be some confusion because I put the code above mainly to illustrate the problem, not to give a working example. [编辑]似乎有些混乱,因为我把上面的代码主要用来说明问题,而不是给出一个有效的例子。 Here's a minimal example that shows the namespace issue:
这是一个显示命名空间问题的最小示例:
# Example 1 : large_vector fits into memory
rm(large_vector)
tryCatch({
large_vector = rep(5, 1000)
}, error = function(e) {
# do stuff to build the vector
large_vector = rep(3, 1000)
})
print(large_vector) # all 5
# Example 2 : pretend large_vector does not fit into memory; solution using parent environment
rm(large_vector)
tryCatch({
stop(); # simulate error
}, error = function(e) {
# do stuff to build the vector
large_vector = rep(3, 1000)
assign('large_vector', large_vector, parent.env(environment()))
})
print(large_vector) # all 3
# Example 3 : pretend large_vector does not fit into memory; namespace issue
rm(large_vector)
tryCatch({
stop(); # simulate error
}, error = function(e) {
# do stuff to build the vector
large_vector = rep(3, 1000)
})
print(large_vector) # does not exist
I would do something like this : 我会做这样的事情:
res <- tryCatch({
large_vector = predict(model, large_data_frame)
}, error = function(e) { # I ran out of memory
ll <- lapply(split(data,seq(1,nrow(large_data_frame),1000)),
function(x)
small_vector = predict(model, x))
return(ll)
})
rm(large_data_frame)
if(is.list(ll))
res <- do.call(rbind,res)
The idea is to return a list of predictions results if you run out of the memory. 如果耗尽内存,我们的想法是返回预测结果列表。
NOTE, i am not sure of the result here, because we don't have a reproducible example. 注意,我不确定这里的结果,因为我们没有可重复的例子。
EDIT: Let's try again: 编辑:我们再试一次:
You can use finally
argument of tryCatch
: 你可以使用
tryCatch
finally
参数:
step<-1000
n<-dim(large_data_frame)[1]
large_vector <- NULL
tryCatch({
large_vector <- predict(model, large_data_frame)
}, error = function(e) { # ran out of memory
for (i in seq(from = 1, to = n, by = step)) {
small_vector <- predict(model, large_data_frame[i:(i+step-1),]) #predict in pieces
save(small_vector,file=paste0("tmpfile",i)) #same pieces
}
rm(large_data_frame) #free memory
},finally={if(is.null(large_vector)){ #if we run out of memory
large_vector<-numeric(n) #make vector
for (i in seq(from = 1, to = n, by = step)){
#collect pieces
load(paste0("tmpfile",i))
large_vector[i:(i+step-1)] <- small_vector
}
}})
Here's a simplified version to see what is going on: 这是一个简化版本,可以看到发生了什么:
large_vector<-NULL
rm(y)
tryCatch({
large_vector <- y
}, error = function(e) {# y is not found
print("error")
},finally={if(is.null(large_vector)){
large_vector<-1
}})
> large_vector
[1] 1
EDIT2: Another tip regarding the scope which could be useful for you (although maybe not in this situation as you didn't want to declare large_vector
beforehand): The <<-
operator, from R-help: 编辑2:关于范围的另一个提示可能对你有用(虽然可能不是在这种情况下因为你不想事先声明
large_vector
): <<-
运算符,来自R-help:
The operators <<- and ->> are normally only used in functions, and cause a search to made through parent environments for an existing definition of the variable being assigned...
运算符<< - 和 - >>通常仅在函数中使用,并导致通过父环境进行搜索以查找正在分配的变量的现有定义...
Therefore you could use above example code like this: 因此,您可以使用上面的示例代码:
large_vector<-NULL
rm(y)
tryCatch({
large_vector <- y
}, error = function(e) {# y is not found
large_vector <<- 1
print("error")
})
> large_vector
[1] 1
The code below is quite self explanatory. 下面的代码非常自我解释。 Indeed the problem is that anything inside the error function is not by default applied to the parent environment.
实际上,问题是错误函数内的任何内容都不会默认应用于父环境。
b=0
B = 0
as explained, this doesn't work:
如上所述,这不起作用:
tryCatch(expr = {stop("error1")}, error=function(e) {b=1})
tryCatch(expr = {stop(“error1”)},error = function(e){b = 1})
bb
SOLUTION 1: assign to the parent environment
解决方案1:分配给父环境
tryCatch(expr = {stop("error2")}, error=function(e) {assign(x = "b", value = 2, envir = parent.env(env = environment()))})
tryCatch(expr = {stop(“error2”)},error = function(e){assign(x =“b”,value = 2,envir = parent.env(env = environment()))})
bb
SOLUTION 2: the most simple (only works if you are assigning to b in both
expr
anderror
)解决方案2:最简单(只有在
expr
和error
中分配给b时才有效)b = tryCatch(expr = {stop("error3")}, error=function(e) {b=3;return(b)})
b = tryCatch(expr = {stop(“error3”)},error = function(e){b = 3; return(b)})
bb
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