How to assign an attribute to a variable stored in a data.table

Question

What is an efficient way to modify a variable or a series of variables in a data.table to add or change attributes? For example, the R Hmisc package label function will add a label attribute to a variable, and make it class "labelled" so that [. and other operators will preserve the label (the package defines [.labelled. Likewise there is Hmisc::units to specify units of measurement. I typically add labels and units by using for example

label(age) <- 'Age at study entry'               # or:
label(mydataframe$age) <- 'Age at study entry'   # or:
mydataframe <- upData(mydataframe, labels=c(age='Age at study entry'), units='year')

data.table is correctly preserving attributes for simple operations:

require(Hmisc)
x1 <- runif(10)
label(x1) <- 'This is a label'
units(x1) <- 'xunits'
x2 <- rnorm(10)
d <- data.table(x1, x2)
label(d$x1)      # label there
label(d[,'x1'])  # label gone
label(d[1:3,]$x1)# label there
label(d[,x1])    # label there
units(d[1:2,x1]) # yes

so the primary question is how to insert attributes into an already existing data.table object with a minimum of memory use/execution time.

What is an example of a typical data.table operation where your labels are not preserved? — s_baldur
– s_baldur, Commented Jun 23, 2020 at 14:10
Great question and I should have addressed that. Will edit top post now. — Frank Harrell
– Frank Harrell, Commented Jun 23, 2020 at 14:14
Note that d[,'x1'] returns a data.table and d[1:3,]$x1 returns the vector... the actual label attribute follows the vector. — s_baldur
– s_baldur, Commented Jun 23, 2020 at 14:20
you can subsribe to this issue to be informed about the feature: github.com/Rdatatable/data.table/issues/623 also you may want to upvote it — jangorecki
– jangorecki, Commented Jun 24, 2020 at 21:22

s_baldur · Accepted Answer · 2020-06-23 14:19:05Z

3

Setting variable attributes (including labels) in data.table:

To easily and efficiently (by reference) set the label you can use: setattr().

Example:

library(data.table)
iDT <- data.table(iris)

setattr(iDT$Species, "label", "Know the species")
attributes(iDT$Species)

# $levels
# [1] "setosa"     "versicolor" "virginica" 
# 
# $class
# [1] "factor"
# 
# $label
# [1] "Know the species"

edited Jun 23, 2020 at 14:19

answered Jun 23, 2020 at 14:08

s_baldur

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6 Comments

Frank Harrell Over a year ago

Wonderful. How would I use the full capabilities of Hmisc::label such that I can provide multiple attributes at once (label and units plus possibly class) so that the attributes will survive subsetting?

s_baldur Over a year ago

I guess you could try something like setattr(iDT$Species, "class", c("factor", "labelled"))? In general I am not convinced attributes are the best place to keep metadata.

Roland Over a year ago

@FrankHarrell Your question is a bit unclear. data.table preserves attributes. I'd suggest you provide a simple setlabel function modeled after this answer for use with data.table (but it could be used elsewhere too).

Frank Harrell Over a year ago

I will try that. It would be nice if a compact syntax would work, i.e., one that looks more like setkey(). I've wondered too whether there is a better place to store metadata, but I've never found one that is safe for subsetting and that doesn't require a bit more bookkeeping.

Frank Harrell Over a year ago

I'm going to modify the R Hmisc package upData function to do setattr in a loop over the variables which are being given labels or units. data.table is blazing fast at doing this.

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