Join 2 data frames using data.table with conditions - r

Question

I have these two data frames:
set.seed(42)
A <- data.table(station = sample(1:10, 1000, replace=TRUE),
hash = sample(letters[1:5], 1000, replace=TRUE),
point = sample(1:24, 1000, replace=TRUE))
B <- data.table(station = sample(1:10, 100, replace=TRUE),
card = sample(letters[6:10], 100, replace=TRUE),
point = sample(1:24, 100, replace=TRUE))
Dataframe A contains more than 1M rows.
I try to find hash (from A) for each card (from B). I have some conditions there: stations and points in A lays in a range(for station +- 1 and for points just + 2).
I use grouping B by card and execute for each group function for binding rows after implementing such conditions and get max by freq.
detect <- function(x){
am0 <- data.frame(station = 0,
hash = 0,
point = 0)
for (i in 1:nrow(x)) {
am1 <- A %>%
filter(station %in% (B$station[i] - 1) : (B$station[i] + 1) &
point > B$point[i] & point < B$point[i] + 2)
am0 <- rbind(am0, am1)
}
t <- as.data.frame(table(am0$hash))
t <- t %>%
arrange(-Freq) %>%
filter(row_number() == 1)
return(t)
}
And then just:
library(dplyr)
B %>%
group_by(card) %>%
do(detect(.)) %>%
ungroup
But I don't know how to implement function by each group with indices [i] so I actually get a wrong result.
# A tibble: 5 x 3
card Var1 Freq
<chr> <fctr> <int>
1 f c 46
2 g c 75
3 h c 41
4 i c 64
5 j c 62
I`m a beginner but I know best solution for big datasets - using data.table library for join 2 datasets like these. Can you help me to find decision for it?

Answer 1

I think what you want to do is:
#### Prepare join limits
B[, point_limit := as.integer(point + 2)]
B[, station_lower := as.integer(station - 1)]
B[, station_upper := as.integer(station + 1)]
## Join A on B, creates All combinations of points in A and B fulfilling the conditions
joined_table <- B[A,
, on = .( point_limit >= point, point <= point,
station_lower <= station, station_upper >= station),
nomatch = 0,
allow.cartesian=TRUE]
## Count the occurrences of the combinations
counted_table <- joined_table[,.N, by=.(card,hash)][order(card, -N)]
## Select the top for each group.
counted_table[, head(.SD, 1 ),by = .(card)][order(card)]
This will create a full table with all the information in and then do the counting on that. It relies purely on data.tables since to fully take advantage of the speed gains from that package. The data.table vignette is good if you are unfamiliar with the syntax. The nomatch condition ensures that we are doing an inner join.
This will probably be fine if A is only 1M rows and B is kept the same size, depending on your datas distribution. We can however split B also in a similar way to your do statement using the package purrr. I'm not sure how this interacts with R:s garabage collection however.
frame_list <- purrr::map(unique(B$card),
~ B[card == .x][A,
, on = .(point_limit >= point,
point <= point,
station_lower <= station,
station_upper >= station),
nomatch = 0,
allow.cartesian = TRUE][, .N, by = .(card, hash)])
counted_table_mem <- rbindlist(frame_list )
Something to note in this is that I use, rbindlist instead of multiple rbind. Repeatedly calling rbind will be very slow, since you will need to allocate new memory each time.