I have two dataset with names and I need to compare names in both datasets. I just need to keep the union of the two datasets based on the names. However, a name is still considered 'matched' if it is part of the another name even if it is not a full match and vice versa. For example, "seb" should match to "seb", but also to "sebas". I am using str_detect(), but it is too slow. I am wondering if there is any way to speed up this process. I tried some other packages and functions, but nothing really improved the speed. I am open for any R or Python solution.
Create two dummy datasets
library(dplyr)
library(stringr)
set.seed(1)
data_set_A <- tibble(name = unique(replicate(2000, paste(sample(letters, runif(1, 3, 10), replace = T), collapse = "")))) %>%
mutate(ID_A = 1:n())
set.seed(2)
data_set_B <- tibble(name_2 = unique(replicate(2000, paste(sample(letters, runif(1, 3, 10), replace = T), collapse = "")))) %>%
mutate(ID_B = 1:n())
Test matching of full matches only
# This is almost instant
data_set_A %>%
rowwise() %>%
filter(any(name %in% data_set_B$name_2) | any(data_set_B$name_2 %in% name)) %>%
ungroup()
# A tibble: 4 x 2
name ID_A
<chr> <int>
1 vnt 112
2 fly 391
3 cug 1125
4 xgv 1280
Include partial matches (This is what I want to optimize)
This of course only gives me the subset of dataset A, but that is ok.
# This takes way too long
data_set_A %>%
rowwise() %>%
filter(any(str_detect(name, data_set_B$name_2)) | any(str_detect(data_set_B$name_2, name))) %>%
ungroup()
A tibble: 237 x 2
name ID_A
<chr> <int>
1 wknrsauuj 2
2 lyw 7
3 igwsvrzpk 16
4 zozxjpu 18
5 cgn 22
6 oqo 45
7 gkritbe 47
8 uuq 92
9 lhwfyksz 94
10 tuw 100
Fuzzyjoin method.
This also works, but is equally slow
bind_rows(
fuzzyjoin::fuzzy_inner_join(
data_set_A,
data_set_B,
by = c("name" = "name_2"),
match_fun = stringr::str_detect
) %>%
select(name, ID_A),
fuzzyjoin::fuzzy_inner_join(
data_set_B,
data_set_A,
by = c("name_2" = "name"),
match_fun = stringr::str_detect
) %>%
select(name, ID_A)
) %>%
distinct()
data.table solution
not much faster unfortunately
library(data.table)
setDT(data_set_A)
setDT(data_set_B)
data_set_A[data_set_A[, .I[any(str_detect(name, data_set_B$name_2)) |
any(str_detect(data_set_B$name_2, name))], by = .(ID_A)]$V1]
from fast partial match checking in R or python or Julia
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