Explanation of subsetting

Question

Can anyone explain what this line t[exists,][1:6,] is doing in the code below and how that subsetting works?

t<-trees
t[1,1]= NA
t[5,3]= NA
t[1:6,]
exists<-complete.cases(t)
exists
t[exists,][1:6,]

Answer 1

The complete.cases function will check the data frame and will return a vector of TRUE and FALSE where a TRUE indicates a row with no missing data. The vector will be as long as there are rows in t.

The t[exits,] part will subset the data so that only rows where exists is true will be considered - the row that have missing data will be FALSE in exists and removed. The [1:6,] will only take the first 6 rows where there is no missing data.

Answer 2

Some background

In R, [ is a function like any other. R parses t[exists, ] as

`[`(t, exists)  # don't forget the backticks!

Indeed you can always call [ with the backtick-and-parentheses syntax, or even crazier use it in constructions like

as.data.frame(lapply(t[exists, ], `[`, 1:6, ))

which, believe it or not, is (almost) equivalent to t[exists,][1:6,].

The same is true for functions like [[, $, and more exotic stuff like names<-, which is a special function to assign argument value to the names attribute of an object. We use functions like this all the time with syntax like

names(iris) <- tolower(names(iris))

without realizing that what we're really doing is

`names(iris)<-`(iris, tolower(names(iris))

And finally, you can type

?`[`

for documentation, or type

`[`

to return the definition, just like any other function.

What t[exists,][1:6,] does

The simple answer is that R parses t[exists,][1:6,] as something like:

1. Get the value of t
2. From the result of step 1, get the rows that correspond to TRUE elements of exists.
3. From the result of step 2, get rows with row numbers in the vector 1:6, i.e. rows 1 through 6

The more complicated answer is that this is handled by the parser as:

`[`(`[`(t, exists, ), 1:6, ) # yes, this has blank arguments

which a human can interpret as

temporary_variable_1 <- `[`(t, exists, )
temporary_variable_2 <- `[`(temporary_variable_1, 1:6, )
print(temporary_variable_2)  # implicitly, sending an object by itself to the console will `print` that object

Interestingly, because you typically can't pass blank arguments in R, certain constructions are impossible with the bracket function, like eval(call("[", t, exists, )) which will throw an undefined columns selected error.