Can't suppress warnings or messages while using nls2::nls2 in R

Question

I'm attempting to fit ~100 data sets to a triexponential decay formula, and the data often don't fit well. That's fine, but I can't seem to suppress the gazillion warnings that this produces. Since this is a part of a markdown script, in the end, I get pages and pages of repetitive warning messages.

Here is an example of my data, which I've named DF:

structure(list(Time_min = c(19, 34, 49, 64, 94, 124, 154, 184, 
214, 244, 304), Concentration = c(477.08, 284.26, 189.16, 134.66, 
74.32, 53.04, 28.16, 16.78, 9.24, 8.7, 4.42)), row.names = c(NA, 
-11L), class = "data.frame")

And here's an example of what I've tried:

StartGuess <- data.frame(A = c(100, 500),
                         alpha = c(0.01, 0.5),
                         B = c(100, 500),
                         beta = c(0.001, 0.05),
                         G = c(10, 100),
                         gamma = c(0.0001, 0.01))

suppressMessages(nls2::nls2(Concentration ~ A * exp(-alpha * Time_min) +
                            B * exp(-beta * Time_min) +
                            G * exp(-gamma * Time_min), 
                      data = DF, start = StartGuess))

suppressWarnings(nls2::nls2(Concentration ~ A * exp(-alpha * Time_min) +
                            B * exp(-beta * Time_min) +
                            G * exp(-gamma * Time_min), 
                      data = DF, start = StartGuess))


suppressWarnings(
      suppressMessages(nls2::nls2(Concentration ~ A * exp(-alpha * Time_min) +
                                  B * exp(-beta * Time_min) +
                                  G * exp(-gamma * Time_min), 
                            data = DF, start = StartGuess)))

No matter how I try suppressing things, I get a loooooooonnnnnggg list of errors such as:

Error in numericDeriv(form[[3L]], names(ind), env) : 
  Missing value or an infinity produced when evaluating the model
Error in (function (formula, data = parent.frame(), start, control = nls.control(),  : 
  singular gradient

To be clear, I'm expecting the messages and errors because I know I often lack sufficient data to adequately describe a triexponential decay, but there should be some way to suppress all these warnings, shouldn't there?

Answer 1

I'm going to suggest a combination of capture.output(type="message", ...) and try(). Just the try() (or tryCatch()) doesn't catch all of the messages, since they are emitted from deeper within nls2::nls2 ...

cc <- capture.output(type="message",
         res <- try(nls2::nls2(Concentration ~ A * exp(-alpha * Time_min) +
                      B * exp(-beta * Time_min) +
                      G * exp(-gamma * Time_min), 
                      data = DF, start = StartGuess),
    silent=TRUE)
)

In this case res ends up as an object of type try-error: you can detect this and do what you want by testing if (inherits(res,"try-error")) ...

[1] "Error in result[[which.min(ss)]] : \n  attempt to select less than one element in get1index\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
<simpleError in result[[which.min(ss)]]: attempt to select less than one element in get1index>