What can be in an R data.frame column?

As an R programmer have you every wondered what can be in a data.frame column?

The documentation is a bit vague, help(data.frame) returns some comforting text including:

Value

A data frame, a matrix-like structure whose columns may be of differing types (numeric, logical, factor and character and so on).

If you ask an R programmer the commonly depended upon properties of a data.frame columns are:

1. All columns in a data frame have the same length. (true, but with an asterisk)
2. All columns in a data frame are vectors with type (see help(typeof)) and class (see help(class)) deriving from one of the primitive types (such as: numeric, logical, factor and character and so on). (FALSE!)
3. (weakening from 2) All items in a single column in a data frame have the same number of items per row index. (FALSE)
4. (weakening from 3) All items in a single column in a data frame are at least homogeneous and have the type/class per row index. (FALSE, or that class/type can be list hiding heterogeneous nested entries)

Unfortunately only for first item is actually true. The data.frame() and as.data.frame() methods try to do some conversions to make more of the items in the above list are usually true. We know data.frame is implemented as a list of columns, but the idea is the class data.frame overrides a lot of operators and should be able to maintain some useful invariants for us.

data.frame is one of R’s flagship types. You would like it to have fairly regular and teachable observable behavior. (Though given the existence of the reviled attach() command I a beginning to wonder if data.frame was a late addition to S, the language R is based on.)

But if you are writing library code (like vtreat) you end up working with the data frames as they are, and not as you would like them to be.

Here is an example of the problem:

d <- data.frame(a=1:3) d$v <- tapply(X=1:6, INDEX=c('a','a','b','b','c','c'), FUN=sum, simplify=TRUE) print(class(d$a)) ## [1] "integer" print(class(d$v)) ## [1] "array"

Even with the simplify=TRUE argument set, tapply() returns an array, and that array type survives when added to a data.frame. There is no implicit as.numeric() conversion to change from an array to a primitive vector class. Any code written under the assumption the columns of the data frame restrict themselves to simple classes and types will fail.

Case in point: earlier versions of vtreat would fail to recognize such a column as numeric (because the library was checking the class name, as I had falsely assumed the is.numeric() check was as fragile as the is.vector() checks) and treat the column as strings. And this is the cost of not having type strictness: there is no way to write concise correct code for dealing with other people’s data. vtreat already had special case code for POSIXlt types (one way nested lists can get into data frames!), but I didn’t have special code to check for lists and arrays in general. It isn’t so much we used the wrong type-check (looking at class() instead of using is.numeric(), which can be debated) it is we failed to put in enough special case code to catch (or at least warn) on all the unexpected corner cases.

This is why I like type systems, they let you document (in a machine readable way, so you can also enforce!) the level of diversity of input you expect. If the inputs are not that diverse they you then have some chance that simple concise code can be correct. If the inputs are a diverse set of unrelated types that don’t share common interfaces, then no concise code can be correct.

Many people say there is no great cost to R’s loose type system, and I say there is. It isn’t just my code. The loose types are why things like ifelse() are 30 lines of code instead of 5 lines of code (try print(ifelse), you will notice the majority of the code is trying to strip off attributes and defend against types that are almost, but not quite what one would expect; only a minority of the code is doing the actual work). This drives up the expense of writing a fitter (such as: lm, glm, randomForest, gbm, rpart, …) as to be correct the fitter may have to convert a number of odd types into primitives. And it drives up the cost of using fitters, as you have to double check the authors anticipated all types you end up sending. And you may not even know which types you are sending due to odd types entering through use of other libraries and functions (such as tapply()).

If your rule of code composition is Postel’s law (instead of checkable types and behavior contracts) you are going to have very bloated code as each module is forced enumerate and correct a large number of “almost the same” behaviors and encodings. You will also have a large number of “rare” bugs as there is no way every library checks all corner cases, and each new programmer accidentally injects a different unexpected type into their work. When there are a large number of rare bugs lurking: then bugs are encountered often and diagnosing them is expensive (as each one feels unique).

When you work with systems that are full of special cases your code becomes infested with the need to handle special cases. Elegance and correctness become opposing goals instead of synergistic achievements.

Okay, I admit arrays are not that big a deal. But arrays are the least of your worries.

Columns of a data frame can be any the following types:

• POSIXlt a complicated list structure, making the column a nested list.
• Arbitrary lists (including ragged lists, and lists with different types in each row).
• Matrices.
• Data frames.

Below is an example of a pretty nasty data frame. Try code() and typeof() on various columns; try str() on various entries; and definitely try the print(unclass(d[1,'xPOSIXlt'])) as it looks like str() hides the awful details in this case (perhaps it or something it depends on is overridden).

d <- data.frame(xInteger=1:3, xNumeric=0, xCharacter='a', xFactor=as.factor('b'), xPOSIXct=Sys.time(), xRaw=raw(3), xLogical=TRUE, xArrayNull=as.array(list(NULL,NULL,NULL)), stringsAsFactors=FALSE) d$xPOSIXlt <- as.POSIXlt(Sys.time()) d$xArray <- as.array(c(7,7,7)) d$xMatrix <- matrix(data=-1,nrow=3,ncol=2) d$xListH <- list(10,20,'thirty') d$xListR <- list(list(),list('a'),list('a','b')) d$xData.Frame <- data.frame(xData.FrameA=6:8,xData.FrameB=11:13) print(colnames(d)) ## [1] "xInteger" "xNumeric" "xCharacter" "xFactor" "xPOSIXct" ## [6] "xRaw" "xLogical" "xArrayNull" "xPOSIXlt" "xArray" ## [11] "xMatrix" "xListH" "xListR" "xData.Frame" print(d) ## xInteger xNumeric xCharacter xFactor xPOSIXct xRaw xLogical ## 1 1 0 a b 2015-04-09 10:40:26 00 TRUE ## 2 2 0 a b 2015-04-09 10:40:26 00 TRUE ## 3 3 0 a b 2015-04-09 10:40:26 00 TRUE ## xArrayNull xPOSIXlt xArray xMatrix.1 xMatrix.2 xListH xListR ## 1 NULL 2015-04-09 10:40:26 7 -1 -1 10 NULL ## 2 NULL 2015-04-09 10:40:26 7 -1 -1 20 a ## 3 NULL 2015-04-09 10:40:26 7 -1 -1 thirty a, b ## xData.Frame.xData.FrameA xData.Frame.xData.FrameB ## 1 6 11 ## 2 7 12 ## 3 8 13 print(unclass(d[1,'xPOSIXct'])) ## [1] 1428601226 print(unclass(d[1,'xPOSIXlt'])) ...

(Note: neither is.numeric(d$xPOSIXct) or is.numeric(d$xPOSIXlt) is true, though both pass nicely through as.numeric(). So even is.numeric() doesn’t signal everything we need to know about the ability to use a column as a numeric quantity.)

(Also notice length(d$xData.Frame) is 2: the number of columns of the sub-data frame. And it is not 3 or nrow(d$xData.Frame). So even the statement “all columns have the same length” needs a bit of an asterisk by it. The columns all have the same length- but not the length returned by the length() method. Also note nrow(c(1,2,3)) return NULL so you can’t use that function everywhere either.)

Related posts:

1. R style tip: prefer functions that return data frames
2. Check your return types when modeling in R
3. R annoyances