I was looking at the source code for the r function expand.grid and noticed a command I don't understand (the last line):
function (..., KEEP.OUT.ATTRS = TRUE, stringsAsFactors = TRUE)
{
nargs <- length(args <- list(...))
if (!nargs)
I am not familiar with this syntax for an if-statement. What is if(!nargs) testing? I tried testing it with something that did exist, and it worked. But it doesn't work with something that doesn't exist...
x <- list(1, 4, 6)
nargs <- length(x)
if(nargs)
print("Success") #This does print "Success" and nargs exists
if(!nargs)
print("Fail") #Doesn't print, as you'd expect
if(!dogs)
print("Success") #Error: object 'dogs' not found
So my guess (that it was an existence test) is wrong, or I am testing it wrong.
!nargs means you are testing the value of nargs is FALSE (or 0 in your case). nargs must exist before testing its value. In your example it does exist.
!dogs is trying to test a non-existing object, so you cannot test its value, object dogs not found is the correct error message there.
Related
x = 1
simple <- function(p,q){
return(q)
}
test = simple(x,y)
Error in simple(x, y) : object 'y' not found
Please Note : Even if I don't create a variable "y", I should not get this error. Instead I want a message to be thrown saying "No data".
You can use try() (or the more elaborate tryCatch() to do this. For example,
x = 1
simple <- function(p,q){
q <- try(force(q), silent = TRUE)
if (inherits(q, "try-error")) {
warning("No data")
q <- NULL
}
return(q)
}
test = simple(x,y)
#> Warning in simple(x, y): No data
Created on 2021-01-28 by the reprex package (v0.3.0)
What the force() function does is evaluate the argument. If that fails, it returns an error: but try() catches that. (You don't actually need to call force(q), it would be enough to use try(q), but I think the explicit version is clearer.)
I have a regression model (lm or glm or lmer ...) and I do fitmodel <- lm(inputs) where inputs changes inside a loop (the formula and the data). Then, if the model function does not produce any warning I want to keep fitmodel, but if I get a warning I want to update the model and I want the warning not printed, so I do fitmodel <- lm(inputs) inside tryCatch. So, if it produces a warning, inside warning = function(w){f(fitmodel)}, f(fitmodel) would be something like
fitmodel <- update(fitmodel, something suitable to do on the model)
In fact, this assignation would be inside an if-else structure in such a way that depending on the warning if(w$message satisfies something) I would adapt the suitable to do on the model inside update.
The problem is that I get Error in ... object 'fitmodel' not found. If I use withCallingHandlers with invokeRestarts, it just finishes the computation of the model with the warning without update it. If I add again fitmodel <- lm(inputs) inside something suitable to do on the model, I get the warning printed; now I think I could try suppresswarnings(fitmodel <- lm(inputs)), but yet I think it is not an elegant solution, since I have to add 2 times the line fitmodel <- lm(inputs), making 2 times all the computation (inside expr and inside warning).
Summarising, what I would like but fails is:
tryCatch(expr = {fitmodel <- lm(inputs)},
warning = function(w) {if (w$message satisfies something) {
fitmodel <- update(fitmodel, something suitable to do on the model)
} else if (w$message satisfies something2){
fitmodel <- update(fitmodel, something2 suitable to do on the model)
}
}
)
What can I do?
The loop part of the question is because I thought it like follows (maybe is another question, but for the moment I leave it here): it can happen that after the update I get another warning, so I would do something like while(get a warning on update){update}; in some way, this update inside warning should be understood also as expr. Is something like this possible?
Thank you very much!
Generic version of the question with minimal example:
Let's say I have a tryCatch(expr = {result <- operations}, warning = function(w){f(...)} and if I get a warning in expr (produced in fact in operations) I want to do something with result, so I would do warning = function(w){f(result)}, but then I get Error in ... object 'result' not found.
A minimal example:
y <- "a"
tryCatch(expr = {x <- as.numeric(y)},
warning = function(w) {print(x)})
Error in ... object 'x' not found
I tried using withCallingHandlers instead of tryCatch without success, and also using invokeRestart but it does the expression part, not what I want to do when I get a warning.
Could you help me?
Thank you!
The problem, fundamentally, is that the handler is called before the assignment happens. And even if that weren’t the case, the handler runs in a different scope than the tryCatch expression, so the handler can’t access the names in the other scope.
We need to separate the handling from the value transformation.
For errors (but not warnings), base R provides the function try, which wraps tryCatch to achieve this effect. However, using try is discouraged, because its return type is unsound.1 As mentioned in the answer by ekoam, ‘purrr’ provides soundly typed functional wrappers (e.g. safely) to achieve a similar effect.
However, we can also build our own, which might be a better fit in this situation:
with_warning = function (expr) {
self = environment()
warning = NULL
result = withCallingHandlers(expr, warning = function (w) {
self$warning = w
tryInvokeRestart('muffleWarning')
})
list(result = result, warning = warning)
}
This gives us a wrapper that distinguishes between the result value and a warning. We can now use it to implement your requirement:
fitmodel = with(with_warning(lm(inputs)), {
if (! is.null(warning)) {
if (conditionMessage(warning) satisfies something) {
update(result, something suitable to do on the model)
} else {
update(result, something2 suitable to do on the model)
}
} else {
result
}
})
1 What this means is that try’s return type doesn’t distinguish between an error and a non-error value of type try-error. This is a real situation that can occur, for example, when nesting multiple try calls.
It seems that you are looking for a functional wrapper that captures both the returned value and side effects of a function call. I think purrr::quietly is a perfect candidate for this kind of task. Consider something like this
quietly <- purrr::quietly
foo <- function(x) {
if (x < 3)
warning(x, " is less than 3")
if (x < 4)
warning(x, " is less than 4")
x
}
update_foo <- function(x, y) {
x <- x + y
foo(x)
}
keep_doing <- function(inputs) {
out <- quietly(foo)(inputs)
repeat {
if (length(out$warnings) < 1L)
return(out$result)
cat(paste0(out$warnings, collapse = ", "), "\n")
# This is for you to see the process. You can delete this line.
if (grepl("less than 3", out$warnings[[1L]])) {
out <- quietly(update_foo)(out$result, 1.5)
} else if (grepl("less than 4", out$warnings[[1L]])) {
out <- quietly(update_foo)(out$result, 1)
}
}
}
Output
> keep_doing(1)
1 is less than 3, 1 is less than 4
2.5 is less than 3, 2.5 is less than 4
[1] 4
> keep_doing(3)
3 is less than 4
[1] 4
Are you looking for something like the following? If it is run with y <- "123", the "OK" message will be printed.
y <- "a"
#y <- "123"
x <- tryCatch(as.numeric(y),
warning = function(w) w
)
if(inherits(x, "warning")){
message(x$message)
} else{
message(paste("OK:", x))
}
It's easier to test several argument values with the code above rewritten as a function.
testWarning <- function(x){
out <- tryCatch(as.numeric(x),
warning = function(w) w
)
if(inherits(out, "warning")){
message(out$message)
} else{
message(paste("OK:", out))
}
invisible(out)
}
testWarning("a")
#NAs introduced by coercion
testWarning("123")
#OK: 123
Maybe you could assign x again in the handling condition?
tryCatch(
warning = function(cnd) {
x <- suppressWarnings(as.numeric(y))
print(x)},
expr = {x <- as.numeric(y)}
)
#> [1] NA
Perhaps not the most elegant answer, but solves your toy example.
Don't put the assignment in the tryCatch call, put it outside. For example,
y <- "a"
x <- tryCatch(expr = {as.numeric(y)},
warning = function(w) {y})
This assigns y to x, but you could put anything in the warning body, and the result will be assigned to x.
Your "what I would like" example is more complicated, because you want access to the expr value, but it hasn't been assigned anywhere at the time the warning is generated. I think you'll have to recalculate it:
fitmodel <- tryCatch(expr = {lm(inputs)},
warning = function(w) {if (w$message satisfies something) {
update(lm(inputs), something suitable to do on the model)
} else if (w$message satisfies something2){
update(lm(inputs), something2 suitable to do on the model)
}
}
)
Edited to add:
To allow the evaluation to proceed to completion before processing the warning, you can't use tryCatch. The evaluate package has a function (also called evaluate) that can do this. For example,
y <- "a"
res <- evaluate::evaluate(quote(x <- as.numeric(y)))
for (i in seq_along(res)) {
if (inherits(res[[i]], "warning") &&
conditionMessage(res[[i]]) == gettext("NAs introduced by coercion",
domain = "R"))
x <- y
}
Some notes: the res list will contain lots of different things, including messages, warnings, errors, etc. My code only looks at the warnings. I used conditionMessage to extract the warning message, but
it will be translated to the local language, so you should use gettext to translate the English version of the message for comparison.
Disclaimer: I'm trying to make someone else's code more user friendly and I'm pretty new to R, so if you see me using mismatched coding conventions, that's why.
I'm trying to write my script's status to the terminal as it goes through a list of files, checking to make sure they are valid before using them as input to a model. Therefore, I need to pass a variable (filename) and status ("looks good") to a function that will concatenate them and write them to the terminal in green. When I test the function like so, it works:
say <- function(words){
cat(green(words))
}
hi <- "Hello"
say(c(hi, "World!"))
# Hello World!
But when I call say() from within the ifelse() that I need to call it from, I get an error I cannot decipher:
FileList = as.data.frame(list.files(path = "./R_ModelInputs_SecondaryData",
pattern = ".tif$", all.files = FALSE,
full.names = FALSE, recursive = FALSE,
ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE))
names(FileList)=c("FileName")
for(NAME in FileList$FilName){
data=raster(paste("./R_ModelInputs_SecondaryData/",NAME,sep=""))
ifelse(nrow(data)!=1737,
say(c(NAME, "has a problem"),
ifelse(ncol(data)!=4008,
say(c(NAME, "has a problem")),
say(c(NAME, "looks good"))
))
}
# Goode_FireBrightness_80_10kMax_20002015.tif looks goodError in ans[!test & ok] <- rep(no, length.out = length(ans))[!test &
# :
# replacement has length zero
# Calls: ifelse -> ifelse
# In addition: Warning message:
# In rep(no, length.out = length(ans)) :
# 'x' is NULL so the result will be NULL
# Execution halted
I've tried googling this error but all I've come up with is that it seems to be from the ifelse() call. This doesn't make sense to me because the fact that it's writing the "looks good" part means that it's successfully navigated both ifelse()'s. I inserted a print() statement at the top of the for loop to ensure that it wasn't throwing the error when it tried to evaluate the ifelse() in the second iteration of my for loop, but that's not what it is, as that print() statement only printed once.
ifelse() should be used when you want to return a vector. It expects to return a vector the same length as your first parameter. Your say() function is returning the value from cat() which just returns NULL. There's no way to make NULL the same length as your test condition. This is throwing the ifelse off.
ifelse should not be used for control flow logic. You should be using a standard if/else here for conditional code execution.
Use
if(nrow(data)!=1737) {
say(c(NAME, "has a problem")
} else if (ncol(data)!=4008) {
say(c(NAME, "has a problem"))
} else {
say(c(NAME, "looks good"))
}
Or do this in a more R-y way like this
ff <- list.files(path = ".", pattern = "\\.tif$", full=TRUE)
r <- lapply(ff, raster)
x <- t(sapply(r, dim))
good <- x[,1] == 1737 & x[,2] == 4008
# good
basename(ff)[good]
# problem
basename(ff)[!good]
R allows for assignment via <- and =.
Whereas there a subtle differences between both assignment operators, there seems to be a broad consensus that <- is the better choice than =, as = is also used as operator mapping values to arguments and thus its use may lead to ambiguous statements. The following exemplifies this:
> system.time(x <- rnorm(10))
user system elapsed
0 0 0
> system.time(x = rnorm(10))
Error in system.time(x = rnorm(10)) : unused argument(s) (x = rnorm(10))
In fact, the Google style code disallows using = for assignment (see comments to this answer for a converse view).
I also almost exclusively use <- as assignment operator. However, the almost in the previous sentence is the reason for this question. When = acts as assignment operator in my code it is always accidental and if it leads to problems these are usually hard to spot.
I would like to know if there is a way to turn off assignment via = and let R throw an error any time = is used for assignment.
Optimally this behavior would only occur for code in the Global Environment, as there may well be code in attached namespaces that uses = for assignment and should not break.
(This question was inspired by a discussion with Jonathan Nelson)
Here's a candidate:
`=` <- function(...) stop("Assignment by = disabled, use <- instead")
# seems to work
a = 1
Error in a = 1 : Assignment by = disabled, use <- instead
# appears not to break named arguments
sum(1:2,na.rm=TRUE)
[1] 3
I'm not sure, but maybe simply overwriting the assignment of = is enough for you. After all, `=` is a name like any other—almost.
> `=` <- function() { }
> a = 3
Error in a = 3 : unused argument(s) (a, 3)
> a <- 3
> data.frame(a = 3)
a
1 3
So any use of = for assignment will result in an error, whereas using it to name arguments remains valid. Its use in functions might go unnoticed unless the line in question actually gets executed.
The lint package (CRAN) has a style check for that, so assuming you have your code in a file, you can run lint against it and it will warn you about those line numbers with = assignments.
Here is a basic example:
temp <- tempfile()
write("foo = function(...) {
good <- 0
bad = 1
sum(..., na.rm = TRUE)
}", file = temp)
library(lint)
lint(file = temp, style = list(styles.assignment.noeq))
# Lint checking: C:\Users\flodel\AppData\Local\Temp\RtmpwF3pZ6\file19ac3b66b81
# Lint: Equal sign assignemnts: found on lines 1, 3
The lint package comes with a few more tests you may find interesting, including:
warns against right assignments
recommends spaces around =
recommends spaces after commas
recommends spaces between infixes (a.k.a. binary operators)
warns against tabs
possibility to warn against a max line width
warns against assignments inside function calls
You can turn on or off any of the pre-defined style checks and you can write your own. However the package is still in its infancy: it comes with a few bugs (https://github.com/halpo/lint) and the documentation is a bit hard to digest. The author is responsive though and slowly making improvements.
If you don't want to break existing code, something like this (printing a warning not an error) might work - you give the warning then assign to the parent.frame using <- (to avoid any recursion)
`=` <- function(...){
.what <- as.list(match.call())
.call <- sprintf('%s <- %s', deparse(.what[[2]]), deparse(.what[[3]]))
mess <- 'Use <- instead of = for assigment '
if(getOption('warn_assign', default = T)) {
stop (mess) } else {
warning(mess)
eval(parse(text =.call), envir = parent.frame())
}
}
If you set options(warn_assign = F), then = will warn and assign. Anything else will throw an error and not assign.
examples in use
# with no option set
z = 1
## Error in z = 1 : Use <- instead of = for assigment
options(warn_assign = T)
z = 1
## Error in z = 1 : Use <- instead of = for assigment
options(warn_assign = F)
z = 1
## Warning message:
## In z = 1 : Use <- instead of = for assigment
Better options
I think formatR or lint and code formatting are better approaches.
I am using stopifnot and I understand it just returns the first value that was not TRUE. I f that is some freaky dynamic expression someone who is not into the custom function cannot really make something out of that. So I would love to add a custom error message. Any suggestions?
Error: length(unique(nchar(check))) == 1 is not TRUE
Basically states that the elements of the vector check do not have the same length.
Is there a way of saying: Error: Elements of your input vector do not have the same length!?
Use stop and an if statement:
if(length(unique(nchar(check))) != 1)
stop("Error: Elements of your input vector do not have the same length!")
Just remember that stopifnot has the convenience of stating the negative, so your condition in the if needs to be the negation of your stop condition.
This is what the error message looks like:
> check = c("x", "xx", "xxx")
> if(length(unique(nchar(check))) != 1)
+ stop("Error: Elements of your input vector do not have the same length!")
Error in eval(expr, envir, enclos) :
Error: Elements of your input vector do not have the same length!
A custom message can be added as a label to your expression:
stopifnot("Elements of your input vector do not have the same length!" =
length(unique(nchar(check))) == 1)
# Error: Elements of your input vector do not have the same length!
The assertive and assertthat packages have more readable check functions.
library(assertthat)
assert_that(length(unique(nchar(check))) == 1)
## Error: length(unique(nchar(check))) == 1 are not all true.
library(assertive)
assert_is_scalar(unique(nchar(check)))
## Error: unique(nchar(check)) does not have length one.
if(!is_scalar(unique(nchar(check))))
{
stop("Elements of check have different numbers of characters.")
}
## Error: Elements of check have different numbers of characters.
Or you could package it up.
assert <- function (expr, error) {
if (! expr) stop(error, call. = FALSE)
}
So you have:
> check = c("x", "xx", "xxx")
> assert(length(unique(nchar(check))) == 1, "Elements of your input vector do not have the same length!")
Error: Elements of your input vector do not have the same length!
What about embedding the stopifnot into tryCatch and then recasting the exception with stop using customized message?
Something like:
tryCatch(stopifnot(...,error=stop("Your customized error message"))
Unlike some other solutions this does not require additional packages. Compared to using if statement combined with stop you retain the performance advantages of stopifnot, when you use new R versions. Since R version 3.5.0 stopifnot evaluates expressions sequentially and stops on first failure.
I would recommend you check out Hadley's testthat package. It allows for intuitive testing: the names of the functions are great and the way you write them is like a sentence -- "I expect that length(unique(nchar(check))) is [exactly|approximately] 1". The errors produced are informative.
See here:
http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf
In your case,
> library(testthat)
> check = c("x", "xx", "xxx")
> expect_that(length(unique(nchar(check))), equals(1))
Error: length(unique(nchar(check))) not equal to 1
Mean relative difference: 2
Also note that you don't have the problem that #Andrie referenced with sometimes having to think about double negatives with stopifnot. I know it seems simple, but it caused me many headaches!
The answers already provided are quite good, and mine is just an addition to that collection. For some people it could be more convenient to use one-liner in form of the following function:
stopifnotinform <- function(..., message = "err") {
args <- list(...)
if (length(args) == 0) {
return(NULL)
}
for (i in 1:length(args)) {
result <- args[[i]]
if (is.atomic(result) && result == FALSE) {
stop(message)
}
}
}
# throws an error
stopifnotinform(is.integer(1L), is.integer(2), message = "Some number(s) provided is not an integer")
# continues with execution
stopifnotinform(is.integer(1L), is.integer(2L), message = "Some number(s) provided is not an integer")
Bear in mind that this solution provides you with only one (common) error message for all parameters in ....
Try this:
same_length <- FALSE
stopifnot("Elements of your input vector do not have the same length!" = same_length)
#> Error : Elements of your input vector do not have the same length!