Is there a way to use tryCatch (or similar) in R as a loop, or to manipulate the expr in the warning argument?

Question

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!

Answer 1

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

Answer 2

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 (eg 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.

Answer 3

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

Answer 4

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.

Answer 5

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.