About Vector Arguments

Introduction

The *apply_byname() family of functions are used internally by many functions in matsbyname. These functions (unaryapply_byname(), binaryapply_byname(), naryapply_byname()) allow additional arguments, besides the matrices that are being transformed, which are passed via .FUNdots. Getting .FUNdots right can be challenging, and this vignette provides some background and explanation to those challenges. After reading this vignette, both callers of these functions and programmers who use these functions will be in a better position to take advantage of the various *apply_byname() functions.

An example

To see how the .FUNdots argument works, let’s make an example function that takes advantage of unaryapply_byname(). mysum() adds entries in matrix a, the result depending upon the value of margin.

mysum <- function(a, margin = c(1, 2)) {
  sum_func <- function(a_mat, margin) {
    # When we get here, we will have a single matrix a
    if (1 %in% margin & 2 %in% margin) {
      return(sum(a_mat))
    }
    if (margin == 1) {
      return(rowSums(a_mat) %>% matrix(nrow = nrow(a_mat)))
    }
    if (margin == 2) {
      return(colSums(a_mat) %>% matrix(ncol = ncol(a_mat)))
    }
  }
  unaryapply_byname(sum_func, a, .FUNdots = list(margin = margin))
}

Structuring mysum() as shown above provides several interesting capabilities. First, mysum() works with single matrices.

m <- matrix(1:4, nrow = 2, byrow = TRUE)
m
#>      [,1] [,2]
#> [1,]    1    2
#> [2,]    3    4
# Works for single matrices
mysum(m, margin = 1)
#>      [,1]
#> [1,]    3
#> [2,]    7
mysum(m, margin = 2)
#>      [,1] [,2]
#> [1,]    4    6
mysum(m, margin = c(1, 2))
#> [1] 10

Second, mysum() works with lists.

# Works for lists of matrices
mysum(list(one = m, two = m), margin = 1)
#> $one
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> $two
#>      [,1]
#> [1,]    3
#> [2,]    7
mysum(list(one = m, two = m), margin = 2)
#> $one
#>      [,1] [,2]
#> [1,]    4    6
#> 
#> $two
#>      [,1] [,2]
#> [1,]    4    6

Finally, mysum() works within data frames.

# Works in data frames and tibbles
DF <- tibble::tibble(mcol = list(m, m, m))
res <- DF %>% 
  dplyr::mutate(
    rsums = mysum(mcol, margin = 1), 
    csums = mysum(mcol, margin = 2)
  )
res$rsums
#> [[1]]
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> [[2]]
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> [[3]]
#>      [,1]
#> [1,]    3
#> [2,]    7
res$csums
#> [[1]]
#>      [,1] [,2]
#> [1,]    4    6
#> 
#> [[2]]
#>      [,1] [,2]
#> [1,]    4    6
#> 
#> [[3]]
#>      [,1] [,2]
#> [1,]    4    6

The problem

In the above examples, margin was only 1 or 2, not c(1, 2) for the list and data frame examples. Let’s see what happens when margin = c(1, 2) and a is a list.

tryCatch(mysum(list(m, m, m), margin = c(1, 2)), 
         error = function(e) {strwrap(e, width = 60)})
#> [1] "Error: In prepare_.FUNdots(), when 'a' is a list, but an"   
#> [2] "entry in '.FUNdots' is not a list, every top-level argument"
#> [3] "in .FUNdots must be NULL or have length = 1 or length ="    
#> [4] "length(a) (= 3). Found length = 2 for argument 'margin',"   
#> [5] "which is not a list. Consider converting argument 'margin'" 
#> [6] "into a list of length 1."

To understand better what is happening, let’s try when the list argument to mysum() has length 2.

mysum(list(m, m), margin = c(1, 2))
#> [[1]]
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> [[2]]
#>      [,1] [,2]
#> [1,]    4    6

margin = c(1, 2) is interpreted by unaryapply_byname() as "use margin = 1 for the first m in the list, and use margin = 2 for the second m in the list.

Now we see why passing margin = c(1, 2) failed for a list of length 3 (list(m, m, m)): unaryapply_byname() applied margin = 1 for the first m, margin = 2 for the second m. But the third m had no margin available for it.

We also see why passing margin = c(1, 2) was successful for a list of length 2 (list(m, m)): unaryapply_byname() applied margin = 1 for the first m, margin = 2 for the second m. In that case, we had exactly as many items in margin (2) as items in the list passed to a (2).

Now that we understand the problem, how do we fix it? In other words, how can we apply margin = c(1, 2) to all entries in list(m, m, m)? Or, better yet, how could we apply margin = 1 to the first m, margin = 2 to the second m, and margin = c(1, 2) to the third m?

The fix

Fixes to the problem identified above can be provided by either the caller or (partially) by the programmer in three ways:

Wrap vector arguments in a list

If the caller is more specific, flexibility is gained. By wrapping c(1, 2) in a list(), the caller indicates “Take this margin (c(1, 2)), replicate it as many times as we have items in our a list, using one c(1, 2) for each item in the list.”

mysum(list(m, m, m), margin = list(c(1, 2)))
#> [[1]]
#> [1] 10
#> 
#> [[2]]
#> [1] 10
#> 
#> [[3]]
#> [1] 10

The caller can also supply different margins for each item in the list of matrices.

mysum(list(m, m, m), margin = list(1, 2, c(1, 2)))
#> [[1]]
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> [[2]]
#>      [,1] [,2]
#> [1,]    4    6
#> 
#> [[3]]
#> [1] 10

But the caller must provide either 1 or length(a) items in the margin argument, else an error is emitted.

tryCatch(mysum(list(m, m, m), margin = list(1, 2)), 
         error = function(e) {strwrap(e, width = 60)})
#> [1] "Error: In prepare_.FUNdots(), when both 'a' and '.FUNdots'"
#> [2] "are lists, each top-level argument in .FUNdots must have"  
#> [3] "length = 1 or length = length(a) (= 3). Found length = 2"  
#> [4] "for argument 'margin', which is a list. Consider wrapping" 
#> [5] "argument 'margin' in a list()."

Use the prep_vector_arg() function

To the extent possible, programmers should remove burdens on users of their functions. So, it would be helpful if there were a way to automatically wrap vector arguments in lists. To that end, matsbyname includes the prep_vector_arg() function. prep_vector_arg() uses heuristics to wrap vector arguments in lists, if needed and when possible.

mysum2() demonstrates the use of prep_vector_arg().

mysum2 <- function(a, margin = c(1, 2)) {
  margin <- prep_vector_arg(a, margin)
  sum_func <- function(a_mat, margin) {
    # When we get here, we will have a single matrix a
    if (1 %in% margin & 2 %in% margin) {
      return(sum(a_mat))
    }
    if (margin == 1) {
      return(rowSums(a_mat) %>% matrix(nrow = nrow(a_mat)))
    }
    if (margin == 2) {
      return(colSums(a_mat) %>% matrix(ncol = ncol(a_mat)))
    }
  }
  unaryapply_byname(sum_func, a, .FUNdots = list(margin = margin))
}

If

then prep_vector_arg() wraps the vector argument (in this case margin) in a list(), thereby relieving the caller of having to remember to make it into a list.

mysum2(list(m, m, m), margin = c(1, 2))
#> [[1]]
#> [1] 10
#> 
#> [[2]]
#> [1] 10
#> 
#> [[3]]
#> [1] 10

Note that if the length of the vector argument is equal to the length of the list in a, the caller’s intention is ambiguous, and the vector argument is passed without modification.

mysum2(list(m, m), margin = c(1, 2))
#> [[1]]
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> [[2]]
#>      [,1] [,2]
#> [1,]    4    6

If the caller wants c(1, 2) to be applied to each item in the a list, the caller must wrap c(1, 2) in a list.

mysum2(list(m, m), margin = list(c(1, 2)))
#> [[1]]
#> [1] 10
#> 
#> [[2]]
#> [1] 10

Use a data frame

The reason prep_vector_arg() cannot always wrap vector arguments in a list is that data frame columns are extracted as vectors when they are atomic.

DF2 <- tibble::tibble(mcol = list(m, m), margin = c(1, 2))
DF2
#> # A tibble: 2 x 2
#>   mcol              margin
#>   <list>             <dbl>
#> 1 <int[,2] [2 × 2]>      1
#> 2 <int[,2] [2 × 2]>      2
DF2$margin %>% class()
#> [1] "numeric"

It would be a mistake to wrap DF2$margin in a list() for the following call to mysum2, because the caller’s intent is clearly "apply margin = 1 for the first row and margin = 2 for the second row.

res2 <- DF2 %>% 
  dplyr::mutate(
    sums = mysum2(mcol, margin = margin)
  )
res2$sums
#> [[1]]
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> [[2]]
#>      [,1] [,2]
#> [1,]    4    6

The good news is that within the context of a data frame, the caller’s intent is unambiguous.

DF3 <- tibble::tibble(mcol = list(m, m, m), margin = list(1, c(1, 2), c(1, 2))) %>% 
  dplyr::mutate(
    sumcol = mysum2(mcol, margin = margin)
  )
DF3$sumcol
#> [[1]]
#>      [,1]
#> [1,]    3
#> [2,]    7
#> 
#> [[2]]
#> [1] 10
#> 
#> [[3]]
#> [1] 10

Summary

Dealing with vector arguments to the various *apply_byname() functions can be tricky. But there are three ways to solve any problems that arise:

This vignette illustrated all three fixes.