match.arg

Lately I’ve been working with a lot of people whose first language is not R, which has given me more of an appreciation for R’s oddities. Some in retrospect were probably ill-advised, like partial matching with $: mtcars$disp
#>  [1] 160.0 160.0 108.0 258.0 360.0 225.0 360.0 146.7 140.8 167.6 167.6
#> [12] 275.8 275.8 275.8 472.0 460.0 440.0  78.7  75.7  71.1 120.1 318.0
#> [23] 304.0 350.0 400.0  79.0 120.3  95.1 351.0 145.0 301.0 121.0
mtcars$di #> [1] 160.0 160.0 108.0 258.0 360.0 225.0 360.0 146.7 140.8 167.6 167.6 #> [12] 275.8 275.8 275.8 472.0 460.0 440.0 78.7 75.7 71.1 120.1 318.0 #> [23] 304.0 350.0 400.0 79.0 120.3 95.1 351.0 145.0 301.0 121.0 mtcars$d    # Bonus points if you knew what this would do.
#> NULL

Some are comparatively weird, but function fine, like that R doesn’t care if keyword arguments come before positional ones; it just extracts keywords first and then matches positions:

mean(x = c(1, NA, 3), 0, TRUE)
#> [1] 2
mean(na.rm = TRUE, c(1, NA, 3))
#> [1] 2

But some are weird, but actually really convenient and great, which brings us to the subject of this post: match.arg.

match.arg is a function that only works in functions, and thus is not itself a function people tend to encounter until they try to write code for other people. (You could use it in functions you write for yourself, but it matters less, for reasons that will become apparent in a moment.) It’s also a function that’s baked into much of R’s DNA, so to speak.

For instance, if you look at the documentation for ?optim, base R’s general-purpose optimization function, its “Usage” section looks like this:

optim(par, fn, gr = NULL, ...,
method = c("Nelder-Mead", "BFGS", "CG", "L-BFGS-B", "SANN",
"Brent"),
lower = -Inf, upper = Inf,
control = list(), hessian = FALSE)

Something there is a little funny: Why is the default of method a vector of six methods? Is it going to run six different ways? The argument documentation seems to suggest otherwise:

method The method to be used. See ‘Details’. Can be abbreviated.

“Details” confirms:

The default method is an implementation of that of Nelder and Mead (1965), that uses only function values and is robust but relatively slow. It will work reasonably well for non-differentiable functions.

It then describes "BFGS", "CG", etc. as alternative methods, which makes sense—the documentation is telling us all the possible alternatives. But there’s still something weird here: Is the default really a vector of length 6? Or is that just a documentation nicety, and the signature of the function actually contains method = "Nelder-Mead"?

A quick investigation reveals that it’s not just a nicety—the actual default is a vector of length 6

args(optim)
#> function (par, fn, gr = NULL, ..., method = c("Nelder-Mead",
#>     "BFGS", "CG", "L-BFGS-B", "SANN", "Brent"), lower = -Inf,
#>     upper = Inf, control = list(), hessian = FALSE)
#> NULL

…but somehow that turns into a default of "Nelder-Mead". How? The culprit is a few lines into the body of the function:

head(optim, 8)
#>
#> 1 function (par, fn, gr = NULL, ..., method = c("Nelder-Mead",
#> 2     "BFGS", "CG", "L-BFGS-B", "SANN", "Brent"), lower = -Inf,
#> 3     upper = Inf, control = list(), hessian = FALSE)
#> 4 {
#> 5     fn1 <- function(par) fn(par, ...)
#> 6     gr1 <- if (!is.null(gr))
#> 7         function(par) gr(par, ...)
#> 8     method <- match.arg(method)

What does

method <- match.arg(method)

do?

Starting at ?match.arg, it tells us it does “argument verification using partial matching”. More particularly,

match.arg matches arg against a table of candidate values as specified by choices, where NULL means to take the first one.1

The “Usage” section confirms that optim definitely isn’t running six methods by default:

match.arg(arg, choices, several.ok = FALSE)

Ok, this seems to make some sense—match.arg checks whether an argument to a function is within a list of possibilities. Let’s try it out:

check_is_us_flag_color <- function(color){
match.arg(color, c("red", "white", "blue"))
}

check_is_us_flag_color("blue")
#> [1] "blue"
tryCatch(
check_is_us_flag_color("orange"),
error = identity
)
#> <simpleError in match.arg(color, c("red", "white", "blue")): 'arg' should be one of "red", "white", "blue">

Ooh, look, we even get informative error messages! How nice.

It’s supposed to do partial matching too. Let’s try:

check_is_fourth_of_july_activity <- function(activity){
match.arg(activity, choices = c(
"barbeque in the park",
"watch fireworks"
))
}

check_is_fourth_of_july_activity("watch fireworks")    # Still works.
#> [1] "watch fireworks"
check_is_fourth_of_july_activity("barbeque")    # Works too!
#> [1] "barbeque in the park"
tryCatch(
check_is_fourth_of_july_activity("watch"),    # Doesn't work. That's good.
error = identity
)
#> <simpleError in match.arg(activity, choices = c("watch a parade", "barbeque in the park",     "watch fireworks")): 'arg' should be one of "watch a parade", "barbeque in the park", "watch fireworks">

This could be useful! It encourages us to use descriptive options like "Nelder-Mead", but if people don’t want to type that all the time, they can just type the unambiguous "Nelder", and that will work fine. Also, such a sophisticated approach still takes very little effort from the person writing the function, which is awfully nice.

If you want to understand the details of precisely how match.arg handles partial matches, the documentation says

Matching is done using pmatch, so arg may be abbreviated.

Clicking through and trying out pmatch shows it’s pretty simple—it’s not fuzzy matching à la agrep, just matching from the beginning of strings.

Ok, now we’ve got a grasp of how match.arg works, but that still doesn’t explain how that line from optim works:

method <- match.arg(method)

There are no choices specified! ?match.arg gives us a hint:

In the one-argument form match.arg(arg), the choices are obtained from a default setting for the formal argument arg of the function from which match.arg was called. (Since default argument matching will set arg to choices, this is allowed as an exception to the ‘length one unless several.ok is TRUE’ rule, and returns the first element.)

There’s a lot going on here. This directly answers one question: What happens if method is not set? In this case, it will return the first element, which is why the default is in fact "Nelder-Mead".

Even if you never use match.arg, this behavior is a good thing to understand, because you’ll see documentation like this everywhere: ?read.table, ?png, ?order, ?t.test, ?ggplot2::position_dodge, ?tidyr::fill, ?data.table::shift, etc., etc., etc.

But there are two possibilities here:

• no argument is passed, and match.arg gets the full length-6 vector, or
• an argument is passed, and match.arg is only passed one string.

Taking the first element of a vector explains how the first possibility works:

check_good_firework <- function(firework = c('bottle rocket', 'roman candle', 'ones that require a license')){
match.arg(firework)
}

check_good_firework()
#> [1] "bottle rocket"

match.arg is passed the full vector for firework, and picks the first one. But is it using that vector for choices? Let’s see:

check_good_firework(c('bottle rocket', 'roman candle', 'ones that require a license'))
#> [1] "bottle rocket"
tryCatch(
check_good_firework(c('snake', 'M80')),
error = identity
)
#> <simpleError in match.arg(firework): 'arg' must be of length 1>

Hmm, so it is getting the choices from somewhere. That’s good, as it explains how the case in which an argument is passed is handled. But where is match.arg getting the options if they aren’t passed to it? The docs, one more time:

In the one-argument form match.arg(arg), the choices are obtained from a default setting for the formal argument arg of the function from which match.arg was called.

Ah, “the formal argument arg of the function from which match.arg was called”. But what’s a “formal argument”? The details get a little hairy2, but essentially formals are the stuff you put in the parentheses after function. There’s even a sensibly-named function to get them, should you need:

str(formals(optim))
#> Dotted pair list of 9
#>  $par : symbol #>$ fn     : symbol
#>  $gr : NULL #>$ ...    : symbol
#>  $method : language c("Nelder-Mead", "BFGS", "CG", "L-BFGS-B", "SANN", "Brent") #>$ lower  : language -Inf
#>  $upper : num Inf #>$ control: language list()
#>  $hessian: logi FALSE Notice this is not quite a normal list—some elements are empty (like par and fn), and ... is actually the name of an element (that doesn’t exist). It is a list, but this is the topsy-turvy world of operating on the language, so this is a pairlist, which only much ever gets used for messing with the structure of functions.3 Regardless, we can see that method is there with its default. The source of match.arg shows how it gets the default to use for choices: head(match.arg, 7) #> #> 1 function (arg, choices, several.ok = FALSE) #> 2 { #> 3 if (missing(choices)) { #> 4 formal.args <- formals(sys.function(sysP <- sys.parent())) #> 5 choices <- eval(formal.args[[as.character(substitute(arg))]], #> 6 envir = sys.frame(sysP)) #> 7 } This code is both complicated and hairy (please don’t use <- in function calls), but we can see that sys.function gets the calling function, and formals extracts the formal arguments. Lines 5-6 extract the argument from those formals. Ignoring the environment-handling stuff, let’s try it out: show_function <- function(x, y = c("foo", "bar")){ sys.function() } show_function() #> function(x, y = c("foo", "bar")){ #> sys.function() #> } fmls <- formals(show_function()) str(fmls) #> Dotted pair list of 2 #>$ x: symbol
#>  $y: language c("foo", "bar") fmls$y    # This is still a language object...
#> c("foo", "bar")
eval(fmls\$y)    # ...so evaluate it to make it a real object
#> [1] "foo" "bar"

Cool! This code explains the remaining mystery of match.arg: When only passed an argument, it grabs the default argument for that parameter and uses it as choices. That also explains why match.arg only works in a function if choices is not specified:

tryCatch(
match.arg(c("bratwurst", "hot dog", "hamburger")),
error = identity
)
#> <simpleError in formal.args[[as.character(substitute(arg))]]: no such index at level 1
#> >

So when should you use match.arg? When you’re writing a function with a parameter that can take one of a fairly small number of string values. In return,

• your function will error informatively if passed an incorrect value (instead of breaking wherever it gets used),
• users get convenient partial-matching,
• if you put the choices as the default, the possible choices will be very clear (to people who know about match.arg), and
• your friends coming from Python will reinforce their belief that R is strange, but will be unable to reproduce the behavior in Python without significant code.

So is R quirky? Yep. But that’s not all bad.

1. This NULL bit is confusing, even if you come back after reading everything. It refers to a call like match.arg(NULL, c("deviled eggs", "potato salad")), but the function rarely gets used that way. The “take the first one” bit matters, though, because this is the behavior if choices isn’t passed, as is explained later.↩︎

2. Technically only closures have formals, not primitive functions. Go read about the difference if you like, but it rarely matters from a user perspective.↩︎

3. Try playing around with alist and you’ll start to see what’s going on.↩︎