CODEWITHSUNDEEP
rtidyversepurrrdbplyr
bheavner
bheavner

Reputation: 549

Using purrr::map2() with dbplyr

I'm trying to select lines from one table ("positons") with values for a particular column ("position") that fall within the ranges defined in another ("my_ranges") table, and then to add a grouping tag from the "my_ranges" table.

I can do this using tibbles and a couple purrr::map2 calls, but the same approach doesn't work with dbplyr database-tibbles. Is this expected behavior, and if so, is there a different approach that I should take to use dbplyr for this kind of task?

Here's my example:

library("tidyverse")
set.seed(42)

my_ranges <-
  tibble(
    group_id = c("a", "b", "c", "d"),
    start = c(1, 7, 2, 25),
    end = c(5, 23, 7, 29)
    )

positions <-
  tibble(
    position = as.integer(runif(n = 100, min = 0, max = 30)),
    annotation = stringi::stri_rand_strings(n = 100, length = 10)
  )

# note: this works as I expect and returns a tibble with 106 obs of 3 variables:
result <- map2(.x = my_ranges$start, .y = my_ranges$end,
             .f = function(x, y) {between(positions$position, x, y)}) %>%
  map2(.y = my_ranges$group_id,
              .f = function(x, y){
                positions %>%
                  filter(x) %>%
                  mutate(group_id = y)}
) %>% bind_rows()

# next, make an in-memory db for testing:
con <- DBI::dbConnect(RSQLite::SQLite(), path = ":memory:")

# copy data to db
copy_to(con, my_ranges, "my_ranges", temporary = FALSE)
copy_to(con, positions, "positions", temporary = FALSE)

# get db-backed tibbles:
my_ranges_db <- tbl(con, "my_ranges")
positions_db <- tbl(con, "positions")

# note: this does not work as I expect, and instead returns a tibble with 0 obsevations of 0 variables:
# database range-based query:
db_result <- map2(.x = my_ranges_db$start, .y = my_ranges_db$end,
                  .f = function(x, y) {
                    between(positions_db$position, x, y)
                    }) %>%
  map2(.y = my_ranges_db$group_id,
       .f = function(x, y){
         positions_db %>%
           filter(x) %>%
           mutate(group_id = y)}
  ) %>% bind_rows()

Upvotes: 3

Views: 1417

Answers (2)

edgararuiz
edgararuiz

Reputation: 675

As long as each iteration creates a table of the same dimensions, then there may be a neat way of pushing the entire operation to the database. The idea is to use both map() and reduce() from purrr. Each tbl_sql() operation is lazy, so we can iterate through them without worrying of sending a bunch of queries, and then we can use union() which will basically append the resulting SQL from each iteration to the next using the UNION clause from the given database. Here's an example:

library(dbplyr, warn.conflicts = FALSE)
library(dplyr, warn.conflicts = FALSE)
library(purrr, warn.conflicts = FALSE)
library(DBI, warn.conflicts = FALSE)
library(rlang, warn.conflicts = FALSE)

con <- DBI::dbConnect(RSQLite::SQLite(), path = ":dbname:")

db_mtcars <- copy_to(con, mtcars)

cyls <- c(4, 6, 8)

all <- cyls %>%
  map(~{
    db_mtcars %>%
      filter(cyl == .x) %>%
      summarise(mpg = mean(mpg, na.rm = TRUE)
      )
  }) %>%
  reduce(function(x, y) union(x, y)) 

all
#> # Source:   lazy query [?? x 1]
#> # Database: sqlite 3.22.0 []
#>     mpg
#>   <dbl>
#> 1  15.1
#> 2  19.7
#> 3  26.7

show_query(all)
#> <SQL>
#> SELECT AVG(`mpg`) AS `mpg`
#> FROM (SELECT *
#> FROM (SELECT *
#> FROM `mtcars`)
#> WHERE (`cyl` = 4.0))
#> UNION
#> SELECT AVG(`mpg`) AS `mpg`
#> FROM (SELECT *
#> FROM (SELECT *
#> FROM `mtcars`)
#> WHERE (`cyl` = 6.0))
#> UNION
#> SELECT AVG(`mpg`) AS `mpg`
#> FROM (SELECT *
#> FROM (SELECT *
#> FROM `mtcars`)
#> WHERE (`cyl` = 8.0))

dbDisconnect(con)

Upvotes: 6

moodymudskipper
moodymudskipper

Reputation: 47300

dbplyr translates R into SQL. Lists don't exist in SQL. map creates lists. Thus it's impossible to translate map into SQL.

Mainly dplyr functions and some base functions are translated, they're working on tidyr functions too as I understood. When using dbplyr try to have an SQL logic in your approach or it will easily break.

Upvotes: 3

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