How to get environment of a variable in R - r

I was wondering if there is anyway to get the environment of a declared variable. Say I already have declared a variable to an environment and want to use that variable's environment to declare a few more variables. Something like getEnv("variable")

Refer to:
http://adv-r.had.co.nz/Environments.html#env-basics
library(pryr)
x <- 5
where("x")
#> <environment: R_GlobalEnv>
where("mean")
#> <environment: base>
The where function is described in the above website. It only finds the first environment the variable appears in, but could easily be modified to find all.

You can get all objects in your workspace with ls(), so you can then check which of those are environments:
envirs <- ls()[sapply(ls(), function(x) is.environment(get(x)))]
I need to use get() there because ls() returns character names of objects rather than the objects themselves. Now given some object x, we want to find which environments it exists in. All we need to do is iterate through each environment in envirs, and check if they contain whatever object we're looking for. Something along the lines of (checking for a variable x):
sapply(envirs, function(e) 'x' %in% ls(envir=get(e)))
Here's a function to do all this:
getEnv <- function(x) {
xobj <- deparse(substitute(x))
gobjects <- ls(envir=.GlobalEnv)
envirs <- gobjects[sapply(gobjects, function(x) is.environment(get(x)))]
envirs <- c('.GlobalEnv', envirs)
xin <- sapply(envirs, function(e) xobj %in% ls(envir=get(e)))
envirs[xin]
}
This is more or less the same as what I did outside the function. gobjects reads from ls(), this time explicitly checking the global environment .GlobalEnv, since it is now within a function.
envirs is the same as before, except now it will check .GlobalEnv as well. xin is storing the names of which environments x was found in. The line:
xobj <- deparse(substitute(x))
Allows object to be tested without quotes e.g. getEnv(x) versus getEnv('x'). That's a matter of preference though, you can change it to accept characters instead.
Here's a few tests.
x1 <- 1
getEnv(x1)
# ".GlobalEnv"
x2 <- 2.1
e2 <- new.env()
assign('x2', 2.2, e2)
getEnv(x2)
# ".GlobalEnv" "e2"
e3 <- new.env()
assign('x3', 3, e3)
getEnv(x3)
# "e3"
This only checks environments created within .GlobalEnv. I'm sure you can work out how to extend it to search across more environments though if you need.
I'm surprised there isn't some in-built function for this. Or maybe there is and I don't know about it. I've never actually needed to do anything like this before so maybe it's not actually surprising.

How about this:
getEnvOf <- function(what, which=rev(sys.parents())) {
for (frame in which)
if (exists(what, frame=frame, inherits=FALSE))
return(sys.frame(frame))
return(NULL)
}
Then we can:
x <- 1
getEnvOf("x")
# <environment: R_GlobalEnv>
getEnvOf("y")
# NULL
f <- function() getEnvOf("x")
f()
# <environment: R_GlobalEnv>
g <- function() { x <- 2; getEnvOf("x") }
g()
# <environment: 0x114c26518>

You can use find, as already suggested in the notes, to search the environment of an object in the searchpath. In case you want to seach in the Function Call Stack you can use exists to look in the sys.frame's.
findFrame <- function(what) {
n <- sys.nframe()-1
Filter(Negate(is.null), lapply(n:0, function(i) {
if(exists(what, sys.frame(i), inherits=FALSE)) sys.frame(i)}))
}
x <- 0
f1 <- function() {
x <- 1
f2()
}
f2 <- function() {
x <- 2
tt <- find("x")
print(sapply(tt, as.environment))
tt <- findFrame("x")
print(tt)
}
a <- new.env(parent=emptyenv())
a$x <- 3
attach(a)
b <- new.env(parent=emptyenv())
b$x <- 4
find("x")
#[1] ".GlobalEnv" "a"
findFrame("x")
#[[1]]
#<environment: R_GlobalEnv>
f1()
#$.GlobalEnv
#<environment: R_GlobalEnv>
#
#$a
#<environment: 0x5576b0c7bb80>
#attr(,"name")
#[1] "a"
#
#[[1]]
#<environment: 0x5576af2fa1f8>
#
#[[2]]
#<environment: 0x5576aedcab20>
#
#[[3]]
#<environment: R_GlobalEnv>
f2()
#$.GlobalEnv
#<environment: R_GlobalEnv>
#
#$a
#<environment: 0x5576b0c7bb80>
#attr(,"name")
#[1] "a"
#
#[[1]]
#<environment: 0x5576b013bef0>
#
#[[2]]
#<environment: R_GlobalEnv>

Related

R: instrument function to capture all assignments

Given a regular R function f, I'd like to be able to create a new function f_debug that acts just like f, but lets me keep track of all the assignments to function-local variables that happened inside it.
For example:
f <- function(x, y) {
z <- x + y
df <- data.frame(z=z)
df
}
# This function doesn't work as intended - would like it to (in the case of `f` above)
# write out a list containing `z` and `df` to an RDS file
capturing <- function(func) {
e <- new.env()
altered <- function(...) {
parent <- parent.frame()
e <- something...(func, environment(), parent, etc., etc.)
result <- func(...)
saveRDS(as.list(e), 'foo.rds')
result
}
environment(func) <- e
altered
}
f_debug <- capturing(f)
I'm not sure whether my knowledge gap to do this is large or small, anyone have a solution?
Solution 1: Steal the function's code
Here's a solution which doesn't return a new function which captures intermediate calculations, but rather calls the given function's code internally. There's some limitations, such as it probably only works with named arguments. Instead of storing the intermediate calculations as an RDS, it attaches them as an attribute.
capturing <- function(fun, ...) {
fun <- match.fun(fun)
code <- body(fun)
parent <- environment(fun)
env <- new.env(parent = parent)
for (val in names(list(...))) {
env[[val]] <- list(...)[[val]]
}
result <- eval(code, envir = env, enclos = parent.frame())
attr(result, "intermediate") <- env
result
}
my_add <- function(x, y) {
z <- x+y
u <- x-y
w <- x*y
x + y
}
intermediates <- function(x) {
attr(x, "intermediate", exact = TRUE)
}
value <- capturing(my_add, x = 1, y = 7)
ls(envir = intermediates(value))
#> [1] "u" "w" "x" "y" "z"
intermediates(value)$x
#> [1] 1
# Created on 2022-02-08 by the reprex package (v2.0.1)
Solution 2: Modify the function's code
One weakness of this solution is that if the chosen function features a call to on.exit(add=FALSE), some additional work needs to be done to modify the function so the internal environment is captured. However, it does work when the function accepts ... arguments.
my_add <- function(x, y) {
z <- x+y
u <- x-y
w <- x*y
x + y
}
insert_capture <- function(code) {
# `<<-` assigns into the global environment if no variable of the given name is found
# while traveling up to the global environment. If you need this assignment to go elsewhere,
# I'd recommend passing in `assign()`. Of course, you could also modify the `on.exit()`
# to use saveRDS.
parse(text=append(deparse(code),
"on.exit(._last_capture <<- environment(), add = TRUE)",
after = 1L))
}
capturing2 <- function(fun) {
fun <- match.fun(fun)
code <- insert_capture(body(fun))
body(fun) <- code
fun
}
my_add2 <- capturing2(my_add)
my_add2(1, 7)
#> [1] 8
ls(envir = ._last_capture)
#> [1] "u" "w" "x" "y" "z"
._last_capture$u
#> [1] -6
Created on 2022-02-08 by the reprex package (v2.0.1)
What you are describing is already implemented in base R with utils::dump.frames, in an even more sophisticated way. It saves the frame (environment) associated with each call in the call stack to an object of class "dump.frames", which you can explore retroactively with utils::debugger as if you had actually run your code under a debugger.
capturing <- function(func, ...) {
cc <- as.call(c(quote(utils::dump.frames), list(...)))
cc <- call("on.exit", cc, add = TRUE)
body(func) <- call("{", cc, body(func))
func
}
capturing injects the call on.exit(utils::dump.frames(...), add = TRUE) into the body of func and returns the modified function.
Here, ... is a list of arguments to dump.frames:
dumpto, a character string giving the name to be used for the "dump.frames" object
to.file, a logical flag indicating whether the "dump.frames" object should be assigned in the global environment or save-ed to paste0(dumpto, ".rda") in the current working directory
include.GlobalEnv, a logical flag indicating whether the global environment should be saved as well
A quick example, which you should try yourself:
tmp <- tempfile()
dir.create(tmp)
cwd <- setwd(tmp)
f <- function(x, y) {
z <- x + y
z + 1
}
g <- capturing(f, dumpto = "zzz", to.file = TRUE)
h <- function(a, b) {
d <- g(a, b)
d + 1
}
h12 <- h(1, 2)
load("zzz.rda")
zzz
## $`h(1, 2)`
## <environment: 0x14c16cb58>
##
## $`#2: g(a, b)`
## <environment: 0x14c16ca40>
##
## attr(,"error.message")
## [1] ""
## attr(,"class")
## [1] "dump.frames"
ls(zzz[[1L]])
## [1] "a" "b"
ls(zzz[[2L]])
## [1] "z" "x" "y"
utils::debugger(zzz)
## Message: Available environments had calls:
## 1: h(1, 2)
## 2: #2: g(a, b)
##
## Enter an environment number, or 0 to exit
## Selection: 2
## Browsing in the environment with call:
## #2: g(a, b)
## Called from: debugger.look(ind)
## Browse[1]> ls()
## [1] "x" "y" "z"
## Browse[1]> x == 1 && y == 2 && z == x + y
## [1] TRUE
## Browse[1]> Q
setwd(cwd)
unlink(tmp, recursive = TRUE)
See ?browser if you are unfamiliar with R's environment browser.
My capturing function has the limitation that on.exit calls in the body of func must also use add = TRUE. If you have written func yourself, then it is not much of a limitation at all, and passing add = TRUE is a good habit anyway.
Ultimately, there is no completely safe way to inject code into functions, but, in an interactive setting, I would say that this level of "unsafety" is fine.

Create new scope inside for loop in R [duplicate]

So consider the following chunk of code which does not work as most people might expect it to
#cartoon example
a <- c(3,7,11)
f <- list()
#manual initialization
f[[1]]<-function(x) a[1]+x
f[[2]]<-function(x) a[2]+x
f[[3]]<-function(x) a[3]+x
#desired result for the rest of the examples
f[[1]](1)
# [1] 4
f[[3]](1)
# [1] 12
#attempted automation
for(i in 1:3) {
f[[i]] <- function(x) a[i]+x
}
f[[1]](1)
# [1] 12
f[[3]](1)
# [1] 12
Note that we get 12 both times after we attempt to "automate". The problem is, of course, that i isn't being enclosed in the function's private environment. All the functions refer to the same i in the global environment (which can only have one value) since a for loop does not seem to create different environment for each iteration.
sapply(f, environment)
# [[1]]
# <environment: R_GlobalEnv>
# [[2]]
# <environment: R_GlobalEnv>
# [[3]]
# <environment: R_GlobalEnv>
So I though I could get around with with the use of local() and force() to capture the i value
for(i in 1:3) {
f[[i]] <- local({force(i); function(x) a[i]+x})
}
f[[1]](1)
# [1] 12
f[[3]](1)
# [1] 12
but this still doesn't work. I can see they all have different environments (via sapply(f, environment)) however they appear to be empty (ls.str(envir=environment(f[[1]]))). Compare this to
for(i in 1:3) {
f[[i]] <- local({ai<-i; function(x) a[ai]+x})
}
f[[1]](1)
# [1] 4
f[[3]](1)
# [1] 12
ls.str(envir=environment(f[[1]]))
# ai : int 1
ls.str(envir=environment(f[[3]]))
# ai : int 3
So clearly the force() isn't working like I was expecting. I was assuming it would capture the current value of i into the current environment. It is useful in cases like
#bad
f <- lapply(1:3, function(i) function(x) a[i]+x)
#good
f <- lapply(1:3, function(i) {force(i); function(x) a[i]+x})
where i is passed as a parameter/promise, but this must not be what's happening in the for-loop.
So my question is: is possible to create this list of functions without local() and variable renaming? Is there a more appropriate function than force() that will capture the value of a variable from a parent frame into the local/current environment?
This isn't a complete answer, partly because I'm not sure exactly what the question is (even though I found it quite interesting!).
Instead, I'll just present two alternative for-loops that do work. They've helped clarify the issues in my mind (in particular by helping me to understand for the first time why force() does anything at all in a call to lapply()). I hope they'll help you as well.
First, here is one that's a much closer equivalent of your properly function lapply() call, and which works for the same reason that it does:
a <- c(3,7,11)
f <- list()
## `for` loop equivalent of:
## f <- lapply(1:3, function(i) {force(i); function(x) a[i]+x})
for(i in 1:3) {
f[[i]] <- {X <- function(i) {force(i); function(x) a[i]+x}; X(i)}
}
f[[1]](1)
# [1] 4
Second, here is one that does use local() but doesn't (strictly- or literally-speaking) rename i. It does, though, "rescope" it, by adding a copy of it to the local environment. In one sense, it's only trivially different from your functioning for-loop, but by focusing attention on i's scope, rather than its name, I think it helps shed light on the real issues underlying your question.
a <- c(3,7,11)
f <- list()
for(i in 1:3) {
f[[i]] <- local({i<-i; function(x) a[i]+x})
}
f[[1]](1)
# [1] 4
Will this approach work for you?
ff<-list()
for(i in 1:3) {
fillit <- parse(text=paste0('a[',i,']+x' ))
ff[[i]] <- function(x) ''
body(ff[[i]])[1]<-fillit
}
It's sort of a lower-level way to construct a function, but it does work "as you want it to."
An alternative for force() that would work in a for-loop local environment is
capture <- function(...) {
vars<-sapply(substitute(...()), deparse);
pf <- parent.frame();
Map(assign, vars, mget(vars, envir=pf, inherits = TRUE), MoreArgs=list(envir=pf))
}
Which can then be used like
for(i in 1:3) {
f[[i]] <- local({capture(i); function(x) a[i]+x})
}
(Taken from the comments in Josh's answer above)

Enclosing variables within for loop

So consider the following chunk of code which does not work as most people might expect it to
#cartoon example
a <- c(3,7,11)
f <- list()
#manual initialization
f[[1]]<-function(x) a[1]+x
f[[2]]<-function(x) a[2]+x
f[[3]]<-function(x) a[3]+x
#desired result for the rest of the examples
f[[1]](1)
# [1] 4
f[[3]](1)
# [1] 12
#attempted automation
for(i in 1:3) {
f[[i]] <- function(x) a[i]+x
}
f[[1]](1)
# [1] 12
f[[3]](1)
# [1] 12
Note that we get 12 both times after we attempt to "automate". The problem is, of course, that i isn't being enclosed in the function's private environment. All the functions refer to the same i in the global environment (which can only have one value) since a for loop does not seem to create different environment for each iteration.
sapply(f, environment)
# [[1]]
# <environment: R_GlobalEnv>
# [[2]]
# <environment: R_GlobalEnv>
# [[3]]
# <environment: R_GlobalEnv>
So I though I could get around with with the use of local() and force() to capture the i value
for(i in 1:3) {
f[[i]] <- local({force(i); function(x) a[i]+x})
}
f[[1]](1)
# [1] 12
f[[3]](1)
# [1] 12
but this still doesn't work. I can see they all have different environments (via sapply(f, environment)) however they appear to be empty (ls.str(envir=environment(f[[1]]))). Compare this to
for(i in 1:3) {
f[[i]] <- local({ai<-i; function(x) a[ai]+x})
}
f[[1]](1)
# [1] 4
f[[3]](1)
# [1] 12
ls.str(envir=environment(f[[1]]))
# ai : int 1
ls.str(envir=environment(f[[3]]))
# ai : int 3
So clearly the force() isn't working like I was expecting. I was assuming it would capture the current value of i into the current environment. It is useful in cases like
#bad
f <- lapply(1:3, function(i) function(x) a[i]+x)
#good
f <- lapply(1:3, function(i) {force(i); function(x) a[i]+x})
where i is passed as a parameter/promise, but this must not be what's happening in the for-loop.
So my question is: is possible to create this list of functions without local() and variable renaming? Is there a more appropriate function than force() that will capture the value of a variable from a parent frame into the local/current environment?
This isn't a complete answer, partly because I'm not sure exactly what the question is (even though I found it quite interesting!).
Instead, I'll just present two alternative for-loops that do work. They've helped clarify the issues in my mind (in particular by helping me to understand for the first time why force() does anything at all in a call to lapply()). I hope they'll help you as well.
First, here is one that's a much closer equivalent of your properly function lapply() call, and which works for the same reason that it does:
a <- c(3,7,11)
f <- list()
## `for` loop equivalent of:
## f <- lapply(1:3, function(i) {force(i); function(x) a[i]+x})
for(i in 1:3) {
f[[i]] <- {X <- function(i) {force(i); function(x) a[i]+x}; X(i)}
}
f[[1]](1)
# [1] 4
Second, here is one that does use local() but doesn't (strictly- or literally-speaking) rename i. It does, though, "rescope" it, by adding a copy of it to the local environment. In one sense, it's only trivially different from your functioning for-loop, but by focusing attention on i's scope, rather than its name, I think it helps shed light on the real issues underlying your question.
a <- c(3,7,11)
f <- list()
for(i in 1:3) {
f[[i]] <- local({i<-i; function(x) a[i]+x})
}
f[[1]](1)
# [1] 4
Will this approach work for you?
ff<-list()
for(i in 1:3) {
fillit <- parse(text=paste0('a[',i,']+x' ))
ff[[i]] <- function(x) ''
body(ff[[i]])[1]<-fillit
}
It's sort of a lower-level way to construct a function, but it does work "as you want it to."
An alternative for force() that would work in a for-loop local environment is
capture <- function(...) {
vars<-sapply(substitute(...()), deparse);
pf <- parent.frame();
Map(assign, vars, mget(vars, envir=pf, inherits = TRUE), MoreArgs=list(envir=pf))
}
Which can then be used like
for(i in 1:3) {
f[[i]] <- local({capture(i); function(x) a[i]+x})
}
(Taken from the comments in Josh's answer above)

deparse(substitute(x)) in lapply?

I would like use a function that uses the standard deparse(substitute(x)) trick within lapply. Unfortunately I just get the argument of the loop back. Here's my completely useless reproducible example:
# some test data
a <- 5
b <- 6
li <- list(a1=a,b2=b)
# my test function
tf <- function(obj){
nm <- deparse(substitute(obj))
res <- list(myName=nm)
res
}
tf(a)
#returns
$myName
[1] "a"
which is fine. If I use lapply I either get [[1L]] or the x argument of an anonymous function.
lapply(li,function(x) tf(x))
# returns
$a1
$a1$myName
[1] "x"
$b2
$b2$myName
[1] "x"
Is there any way to obtain the following?
$a1
$a1$myName
[1] "a1"
$b2
$b2$myName
[1] "b1"
If there's anything more general on deparse(substitute(x)) and lapply I'd also eager to know.
EDIT:
The problem as opposed to using an anonymous function that accepts multiple arguments and can thus use the name of the object and the object itself does not work because, the tf function will only accept one argument. So this does not work here...
A possible solution :
lapply(li, function(x) {
call1 <- sys.call(1)
call1[[1]] <- as.name("names")
call1 <- call1[1:2]
nm <- eval(call1)
y <- deparse(substitute(x))
y <- gsub("\\D", "", y)
y <- as.numeric(y)
list(myname=nm[y])
})

using substitute to get argument name with

I'm trying to get the names of arguments in the global environment within a function. I know I can use substitute to get the name of named arguments, but I would like to be able to do the same thing with ... arguments. I kinda got it to work for the first element of ... but can't figure out how to do it for the rest of the elements. Any idea how to get this working as intended.
foo <- function(a,...)
{
print(substitute(a))
print(eval(enquote(substitute(...))))
print(sapply(list(...),function(x) eval(enquote(substitute(x)),env=.GlobalEnv)))
}
x <- 1
y <- 2
z <- 3
foo(x,y,z)
x
y
[[1]]
X[[1L]]
[[2]]
X[[2L]]
The canonical idiom here is deparse(substitute(foo)), but the ... needs slightly different processing. Here is a modification that does what you want:
foo <- function(a, ...) {
arg <- deparse(substitute(a))
dots <- substitute(list(...))[-1]
c(arg, sapply(dots, deparse))
}
x <- 1
y <- 2
z <- 3
> foo(x,y,z)
[1] "x" "y" "z"
I would go with
foo <- function(a, ...) {
print( n <- sapply(as.list(substitute(list(...)))[-1L], deparse) )
n
}
Then
foo(x,y,z)
# [1] "y" "z"
Related question was previously on StackOverflow:
How to use R's ellipsis feature when writing your own function? Worth reading.
Second solution, using match.call
foo <- function(a, ...) {
sapply(match.call(expand.dots=TRUE)[-1], deparse)
}

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