r data.table usage in function call

Question

I want to perform a data.table task over and over in a function call: Reduce number of levels for large categorical variables My problem is similar to Data.table and get() command (R) or pass column name in data.table using variable in R but I can't get it to work

Without a function call this works just fine:

# Load data.table
require(data.table)

# Some data
set.seed(1)
dt <- data.table(type = factor(sample(c("A", "B", "C"), 10e3, replace = T)),
                 weight = rnorm(n = 10e3, mean = 70, sd = 20))

# Decide the minimum frequency a level needs...
min.freq <- 3350

# Levels that don't meet minumum frequency (using data.table)
fail.min.f <- dt[, .N, type][N < min.freq, type]

# Call all these level "Other"
levels(dt$type)[fail.min.f] <- "Other"

but wrapped like

reduceCategorical <- function(variableName, min.freq){
  fail.min.f <- dt[, .N, variableName][N < min.freq, variableName]
  levels(dt[, variableName][fail.min.f]) <- "Other"
}

I only get errors like:

 reduceCategorical(dt$x, 3350)
Fehler in levels(df[, variableName][fail.min.f]) <- "Other" : 
 trying to set attribute of NULL value

And sometimes

Error is: number of levels differs

It is always better to use a `data.table` syntax when working with `data.table`.... — David Arenburg, Aug 22 '16 at 08:00
What are you referring to? `df[, variableName][fail.min.f]` is correct data.table isn't it? — Georg Heiler, Aug 22 '16 at 08:01
No, it's not correct way to work with factors. You could do this in two steps, but I haven't tested for efficiency: `dt[type %in% fail.min.f, type := "Other"]; dt[, type := factor(type)]` I'll try to think of a better way though — David Arenburg, Aug 22 '16 at 08:10
Strange - your method is setting all values in the type column to Other. — Georg Heiler, Aug 22 '16 at 08:20
No it's not.... Btw, your function doesn't have a `df` variable and you should be aware that `:=` modifies data.tables within functions too — David Arenburg, Aug 22 '16 at 08:22
In single use case, your solution works just fine. But within the function everything is marked as Other. — Georg Heiler, Aug 22 '16 at 08:31
Thanks a lot - that works. Which one of the two would you recommend? — Georg Heiler, Aug 22 '16 at 08:48
Why does the last variant only work if everything is in a single line? — Georg Heiler, Aug 22 '16 at 10:18
Not sure what you mean. You could break it to lined where `;` is and remove it — David Arenburg, Aug 22 '16 at 10:21
Indeed that's what I tried but then everything was labelled as "other" — Georg Heiler, Aug 22 '16 at 10:21
It modifies everything in place. Once you run it once, your data set will be already modified *in place*. The second time you'll run it, it will be already on the previously modified data set. If you don't want to modify in place just use the base R syntax: `f — David Arenburg, Aug 22 '16 at 10:24
@DAvid do you want to write your last function as "the solution" ? — Georg Heiler, Aug 22 '16 at 10:31
Why, you like the base R solution best? So why do you need the `data.table` package here in the first place :) — David Arenburg, Aug 22 '16 at 10:32
sorry - I did mean the one from 19 mins ago with data.table ;) But choose the one you see fit. I will go with the data.table version. — Georg Heiler, Aug 22 '16 at 10:34
Btw, do you insist on `factors`? You could do the whole process in a single simple line if `type` were a `character`. Something like `dt[, type := as.character(type)] ; dt[, type := if(.N < min.freq) "other", by = type]` — David Arenburg, Aug 22 '16 at 10:58
Let us [continue this discussion in chat](http://chat.stackoverflow.com/rooms/121542/discussion-between-geoheil-and-david-arenburg). — Georg Heiler, Aug 22 '16 at 14:34

David Arenburg · Accepted Answer · 2016-08-23T12:22:56.387

One possibility is to define your own re-leveling function using data.table::setattr that will modify dt in place. Something like

DTsetlvls <- function(x, newl)  
   setattr(x, "levels", c(setdiff(levels(x), newl), rep("other", length(newl))))

Then use it within another predefined function

f <- function(variableName, min.freq){
  fail.min.f <- dt[, .N, by = variableName][N < min.freq, get(variableName)]
  dt[, DTsetlvls(get(variableName), fail.min.f)]
  invisible()
}

f("type", min.freq)
levels(dt$type)
# [1] "C"     "other"

Some other data.table alternatives

f <- function(var, min.freq) {
  fail.min.f <- dt[, .N, by = var][N < min.freq, get(var)]
  dt[get(var) %in% fail.min.f, (var) := "Other"]
  dt[, (var) := factor(get(var))]
}

Or using set/.I

f <- function(var, min.freq) {
  fail.min.f <- dt[, .I[.N < min.freq], by = var]$V1
  set(dt, fail.min.f, var, "other")
  set(dt, NULL, var, factor(dt[[var]]))
}

Or combining with base R (doesn't modify original data set)

f <- function(df, variableName, min.freq){
  fail.min.f <- df[, .N, by = variableName][N < min.freq, get(variableName)]
  levels(df$type)[fail.min.f] <- "Other"
  df
}

Alternatively, we could stick we characters instead (if type is a character), you could simply do

f <- function(var, min.freq) dt[, (var) := if(.N < min.freq) "other", by = var]

score 1 · Answer 2 · answered Aug 22 '16 at 07:55

1

You are referencing things little differently in the wrapper, to get "type" column name you are using the whole variableName which is actually a vector same with getting levels, you are not using variableName directly as done in function

The error is because value of fail.min.f is coming NULL owing to referencing.

answered Aug 22 '16 at 07:55

wololo

335
2
12

I used dt$x e.g. the whole name in order to prevent the error of using `reduceCategorical('x', 3350)` which results in the following error: In `[ – Georg Heiler Aug 22 '16 at 07:58
In case `fail.min.f` is the last statement - it is not null and prints the desired result. – Georg Heiler Aug 22 '16 at 07:59

r data.table usage in function call

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