Filter rows by function by values โโof each row, data.table
Switching from data.frame syntax to data.table syntax still isn't smooth for me. I thought the following should be trivial, but no. What am I doing wrong here:
> DT = data.table(x=rep(c("a","b","c"),each=3), y=c(1,3,6), v=1:9)
> DT
x y v
1: a 1 1
2: a 3 2
3: a 6 3
4: b 1 4
5: b 3 5
6: b 6 6
7: c 1 7
8: c 3 8
9: c 6 9
I need something like this:
cols = c("y", "v") # a vector of column names or indexes
DT[rowSums(cols) > 5] # Take only rows where
# values at colums y and v satisfy a condition. 'rowSums' here is just an
# example it can be any function that return TRUE or FALSE when applied
# to values of the row.
This works, but what if I want to provide dynamic column names? and my tables have many columns?
>DT[eval( quote(y + v > 5))] #and the following command gives the same result
> DT[y + v > 5]
x y v
1: a 6 3
2: b 3 5
3: b 6 6
4: c 1 7
5: c 3 8
6: c 6 9
> DT[lapply(.SD, sum) > 5, .SDcols = 2:3] # Want the same result as above
Empty data.table (0 rows) of 3 cols: x,y,v
> DT[lapply(.SD, sum) > 5, ,.SDcols = 2:3]
Empty data.table (0 rows) of 3 cols: x,y,v
> DT[lapply(.SD, sum) > 5, , .SDcols = c("y", "v")]
Empty data.table (0 rows) of 3 cols: x,y,v
Update after answers Since it turns out there are many ways to do this, I want to see which one is the best performer. Below is a sample sync code:
nr = 1e7
DT = data.table(x=sample(c("a","b","c"),nr, replace= T),
y=sample(2:5, nr, replace = T), v=sample(1:9, nr, T))
threshold = 5
cols = c("y", "v")
col.ids = 2:3
filter.methods = 'DT[DT[, rowSums(.SD[, cols, with = F]) > threshold]]
DT[DT[, rowSums(.SD[, col.ids, with = F]) > threshold]]
DT[DT[, rowSums(.SD) > threshold, .SDcols = cols]]
DT[DT[, rowSums(.SD) > threshold, .SDcols = c("y", "v")]]
DT[DT[, rowSums(.SD) > threshold, .SDcols = col.ids]]
DT[ ,.SD[rowSums(.SD[, col.ids, with = F]) > threshold]]
DT[ ,.SD[rowSums(.SD[, cols, with = F]) > threshold]]
DT[, .SD[rowSums(.SD) > threshold], .SDcols = cols, by = x]
DT[, .SD[rowSums(.SD) > threshold], .SDcols = col.ids, by = x]
DT[, .SD[rowSums(.SD) > threshold], .SDcols = c("y", "v"), by = x]
DT[Reduce(`+`,eval(cols))>threshold]
DT[Reduce(`+`, mget(cols)) > threshold]
'
fm <- strsplit(filter.methods, "\n")
fm <- unlist(fm)
timing = data.frame()
rn = NULL
for (e in sample(fm, length(fm))) {
# Seen some weird pattern with first item in 'fm', so scramble it
rn <- c(rn, e)
if (e == "DT[Reduce(`+`,eval(cols))>threshold]") {
cols = quote(list(y, v))
} else {
cols = c("y", "v")
}
tm <- system.time(eval(parse(text = e)))
timing <- rbind(timing,
data.frame(
as.list(tm[c("user.self", "sys.self", "elapsed")])
)
)
}
rownames(timing) <- rn
timing[order(timing$elapsed),]
### OUTPUT ####
# user.self sys.self elapsed
# DT[Reduce(`+`,eval(cols))>threshold] 0.416 0.168 0.581
# DT[Reduce(`+`, mget(cols)) > threshold] 0.412 0.172 0.582
# DT[DT[, rowSums(.SD) > threshold, .SDcols = cols]] 0.572 0.316 0.889
# DT[DT[, rowSums(.SD) > threshold, .SDcols = col.ids]] 0.568 0.320 0.889
# DT[DT[, rowSums(.SD) > threshold, .SDcols = c("y", "v")]] 0.576 0.316 0.890
# DT[ ,.SD[rowSums(.SD[, col.ids, with = F]) > threshold]] 0.648 0.404 1.052
# DT[DT[, rowSums(.SD[, cols, with = F]) > threshold]] 0.688 0.368 1.052
# DT[DT[, rowSums(.SD[, col.ids, with = F]) > threshold]] 0.612 0.440 1.053
# DT[ ,.SD[rowSums(.SD[, cols, with = F]) > threshold]] 0.692 0.368 1.058
# DT[, .SD[rowSums(.SD) > threshold], .SDcols = c("y", "v"), by = x] 0.800 0.448 1.248
# DT[, .SD[rowSums(.SD) > threshold], .SDcols = col.ids, by = x] 0.836 0.412 1.248
# DT[, .SD[rowSums(.SD) > threshold], .SDcols = cols, by = x] 0.836 0.416 1.249
Thus, the speed champion:
DT[Reduce(`+`,eval(cols))>threshold]
DT[Reduce(`+`, mget(cols)) > threshold]
I prefer one of mine mget
. And I think the reason is that others are slower because they name rowSums
, whereas it Reduce
only helps to shape the expression. Sincere thanks to everyone who gave the answers. I find it difficult to decide, for me to choose the answer "accept". Reduce
- very specific to this operation sum
, but rowSums
- an example of using an arbitrary function.
cols = c("y", "v")
Try
DT[DT[, rowSums(.SD[, cols, with = F]) > 5]]
or
DT[DT[, rowSums(.SD[, 2:3, with = F]) > 5]]
or
DT[DT[, rowSums(.SD) > 5, .SDcols = cols]]
or
DT[DT[, rowSums(.SD) > 5, .SDcols = c("y", "v")]]
or
DT[DT[, rowSums(.SD) > 5, .SDcols = 2:3]]
or
DT[ ,.SD[rowSums(.SD[, 2:3, with = F]) > 5]]
or
DT[ ,.SD[rowSums(.SD[, cols, with = F]) > 5]]
or
DT[, .SD[rowSums(.SD) > 5], .SDcols = cols, by = x]
or
DT[, .SD[rowSums(.SD) > 5], .SDcols = 2:3, by = x]
or
DT[, .SD[rowSums(.SD) > 5], .SDcols = c("y", "v"), by = x]
Each result will be
# x y v
# 1: a 6 3
# 2: b 3 5
# 3: b 6 6
# 4: c 1 7
# 5: c 3 8
# 6: c 6 9
Some explanations:
-
.SD
is also an objectdata.table
that can work in the fieldDT
. So this lineDT[ ,rowSums(.SD[, cols, with = F]) > 5]
will return a boolean vector indicating in which cases itDT
hasy + v > 5
. So we will add another oneDT
to select those indices insideDT
-
When you use
.SDcols
, it will limit to.SD
only those columns. This way, if you only do something likeDT[, .SD[rowSums(.SD) > 5], .SDcols = 2:3]
, you will lose the columnx
the way it was addedby = x
. -
Another option when using
.SDcols
is to return a boolean vector and then insert it into anotherDT
Here's another possibility:
cols <- quote(list(y, v))
DT[Reduce(`+`,eval(cols))>5]
Or, if you prefer to store cols
as a character vector:
cols <- c('y', 'v')
DT[Reduce(`+`, mget(cols)) > 5]
One of the methods:
cols <- quote(list(y, v))
DT[DT[,Reduce(`+`,eval(cols))>5]]
# x y v
# 1: a 6 3
# 2: b 3 5
# 3: b 6 6
# 4: c 1 7
# 5: c 3 8
# 6: c 6 9