Improving the CompressedList constructors

[LTLA]

I frequently use CompressedLists but I can't figure out how to create them without making a list first. This is a common pattern:

stuff <- runif(100)
f <- sample(10, length(stuff), replace=TRUE)
library(IRanges)
out <- NumericList(split(stuff, f))

This is unfortunate because it spends time creating a large list with lots of little vectors before unlisting everything again to create the CompressedList. It seems like we could easily circumvent the middleman, possibly with an interface like:

CompressedList(stuff, by=f)

This would handle the reordering to create the internal IRanges and the unlistData. It would also handle the type dispatch so that I don't have to explicitly call NumericList for numeric values, etc. Finally, if by=NULL, it would do the same as as(stuff, "CompressedList"), which allows for a slightly less verbose way to convert vectors into CompressedLists:

library(IRanges)
df <- DataFrame(x=runif(100), y=runif(100))
f <- sample(letters, 100, replace=TRUE)
out <- split(df, f)
out[as(which.max(out[,'x']), "CompressedList")]
# replace with out[CompressedList(which.max(out[,'x']))]

[lawremi]

I think splitAsList() should get you most of the way. For the final use case, of converting a list to a CompressedList, I'd prefer the "as" notion over construction, because it's a conversion, analogous to as.list().

[hpages]

@LTLA Depending on your use case, relist() and extractList() are also efficient ways to generate CompressedList objects, in addition to splitAsList().

@lawremi Looks like which.max() is broken on CompressedNumericList objects:

x <- NumericList(a=c(0.1, 0.9), b=c(2.1, 2.9, 1))
which.max(x)
# a b 
# 1 1 

The culprit seems to be this line

IRanges/src/CompressedAtomicList_utils.c

Line 147 in 52b13bf

PARTITIONED_AGG(int, ACCESSOR, INTSXP, INTEGER, \

where int is passed to the PARTITIONED_AGG() macro, with the consequence that values in x are extracted as integer values. Apparently it's been broken since which.min() and which.max() got optimized in 2016 (commit c320278).

[LTLA]

splitAsList() is quite satisfactory.

[hpages]

Looks like we can close this. (@lawremi I moved the which.min() / which.max() story to its own issue.)