Surprising that this wasn't noticed before, or perhaps I'm not following some recommended idiom to drop levels when using data.table. The following code illustrates the bug clearly: The bug remains regardless of whether I use "subset" or simply use dt1 = dt[ name != 'a' ].
d <- data.table(name = c('a','b','c'), value = 1:3)
dt <- data.table(d)
setkey(dt,'name')
dt1 <- subset(dt,name != 'a') # or dt1 <- dt[ name != 'a' ]
> dt1
name value
[1,] b 2
[2,] c 3
> droplevels(dt1)
name value
[1,] b 1
[2,] c 3
--
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