The goal of duckplyr is to provide a drop-in replacement for dplyr that uses DuckDB as a backend for fast operation. DuckDB is an in-process SQL OLAP database management system.
duckplyr also defines a set of generics that provide a low-level implementerโs interface for dplyrโs high-level user interface.
Install duckplyr from CRAN with:
install.packages("duckplyr")
You can also install the development version of duckplyr from R-universe:
install.packages('duckplyr', repos = c('https://duckdblabs.r-universe.dev', 'https://cloud.r-project.org'))
Or from GitHub with:
# install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pak("duckdblabs/duckplyr")
library(conflicted) library(duckplyr) conflict_prefer("filter", "duckplyr") #> [conflicted] Will prefer duckplyr::filter over #> any other package.
There are two ways to use duckplyr.
- To enable duckplyr for individual data frames, use
as_duckplyr_df()as the first step in your pipe. - To enable duckplyr for the entire session, use
methods_overwrite().
The examples below illustrate both methods. See also the companion demo repository for a use case with a large dataset.
This example illustrates usage of duckplyr for individual data frames.
Use as_duckplyr_df() to enable processing with duckdb:
out <- palmerpenguins::penguins %>% # CAVEAT: factor columns are not supported yet mutate(across(where(is.factor), as.character)) %>% as_duckplyr_df() %>% mutate(bill_area = bill_length_mm * bill_depth_mm) %>% summarize(.by = c(species, sex), mean_bill_area = mean(bill_area)) %>% filter(species != "Gentoo")
The result is a data frame or tibble, with its own class.
class(out) #> [1] "duckplyr_df" "tbl_df" "tbl" "data.frame" names(out) #> [1] "species" "sex" "mean_bill_area"
duckdb is responsible for eventually carrying out the operations. Despite the late filter, the summary is not computed for the Gentoo species.
out %>% explain() #> โโโโโโโโโโโโโโโโโโโโโโโโโโโโโ #> โ ORDER_BY โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ ORDERS: โ #> โ dataframe_42_42 โ #> โ 42.___row_number ASC โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ FILTER โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ (species != 'Gentoo') โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ EC: 344 โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ STREAMING_WINDOW โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ ROW_NUMBER() OVER () โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ ORDER_BY โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ ORDERS: โ #> โ dataframe_42_42 โ #> โ 42.___row_number ASC โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ HASH_GROUP_BY โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ #0 โ #> โ #1 โ #> โ min(#2) โ #> โ mean(#3) โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ PROJECTION โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ species โ #> โ sex โ #> โ ___row_number โ #> โ bill_area โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ STREAMING_WINDOW โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ ROW_NUMBER() OVER () โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ PROJECTION โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ species โ #> โ sex โ #> โ bill_area โ #> โโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโ #> โโโโโโโโโโโโโโโดโโโโโโโโโโโโโโ #> โ R_DATAFRAME_SCAN โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ data.frame โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ species โ #> โ bill_length_mm โ #> โ bill_depth_mm โ #> โ sex โ #> โ โ โ โ โ โ โ โ โ โ โ โ โ #> โ EC: 344 โ #> โโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
All data frame operations are supported. Computation happens upon the first request.
out$mean_bill_area #> materializing: #> --------------------- #> --- Relation Tree --- #> --------------------- #> Projection [species as species, sex as sex, mean_bill_area as mean_bill_area] #> Order [___row_number ASC] #> Filter [!=(species, 'Gentoo')] #> Projection [species as species, sex as sex, mean_bill_area as mean_bill_area, row_number() OVER () as ___row_number] #> Projection [species as species, sex as sex, mean_bill_area as mean_bill_area] #> Order [___row_number ASC] #> Aggregate [species, sex, min(___row_number), mean(bill_area)] #> Projection [species as species, island as island, bill_length_mm as bill_length_mm, bill_depth_mm as bill_depth_mm, flipper_length_mm as flipper_length_mm, body_mass_g as body_mass_g, sex as sex, "year" as year, bill_area as bill_area, row_number() OVER () as ___row_number] #> Projection [species as species, island as island, bill_length_mm as bill_length_mm, bill_depth_mm as bill_depth_mm, flipper_length_mm as flipper_length_mm, body_mass_g as body_mass_g, sex as sex, "year" as year, *(bill_length_mm, bill_depth_mm) as bill_area] #> r_dataframe_scan(0xdeadbeef) #> #> --------------------- #> -- Result Columns -- #> --------------------- #> - species (VARCHAR) #> - sex (VARCHAR) #> - mean_bill_area (DOUBLE) #> #> [1] 770.2627 656.8523 694.9360 819.7503 984.2279
After the computation has been carried out, the results are available immediately:
out #> # A tibble: 5 ร 3 #> species sex mean_bill_area #> <chr> <chr> <dbl> #> 1 Adelie male 770. #> 2 Adelie female 657. #> 3 Adelie NA 695. #> 4 Chinstrap female 820. #> 5 Chinstrap male 984.
This example illustrates usage of duckplyr for all data frames in the R session.
Use methods_overwrite() to enable processing with duckdb for all data frames:
methods_overwrite() #> โน Overwriting dplyr methods with duckplyr #> methods
This is the same query as above, without as_duckplyr_df():
out <- palmerpenguins::penguins %>% # CAVEAT: factor columns are not supported yet mutate(across(where(is.factor), as.character)) %>% mutate(bill_area = bill_length_mm * bill_depth_mm) %>% summarize(.by = c(species, sex), mean_bill_area = mean(bill_area)) %>% filter(species != "Gentoo")
The result is a plain tibble now:
class(out) #> [1] "tbl_df" "tbl" "data.frame"
Querying the number of rows also starts the computation:
nrow(out) #> materializing: #> --------------------- #> --- Relation Tree --- #> --------------------- #> Projection [species as species, sex as sex, mean_bill_area as mean_bill_area] #> Order [___row_number ASC] #> Filter [!=(species, 'Gentoo')] #> Projection [species as species, sex as sex, mean_bill_area as mean_bill_area, row_number() OVER () as ___row_number] #> Projection [species as species, sex as sex, mean_bill_area as mean_bill_area] #> Order [___row_number ASC] #> Aggregate [species, sex, min(___row_number), mean(bill_area)] #> Projection [species as species, island as island, bill_length_mm as bill_length_mm, bill_depth_mm as bill_depth_mm, flipper_length_mm as flipper_length_mm, body_mass_g as body_mass_g, sex as sex, "year" as year, bill_area as bill_area, row_number() OVER () as ___row_number] #> Projection [species as species, island as island, bill_length_mm as bill_length_mm, bill_depth_mm as bill_depth_mm, flipper_length_mm as flipper_length_mm, body_mass_g as body_mass_g, sex as sex, "year" as year, *(bill_length_mm, bill_depth_mm) as bill_area] #> r_dataframe_scan(0xdeadbeef) #> #> --------------------- #> -- Result Columns -- #> --------------------- #> - species (VARCHAR) #> - sex (VARCHAR) #> - mean_bill_area (DOUBLE) #> [1] 5
Restart R, or call methods_restore() to revert to the default dplyr implementation.
methods_restore() #> โน Restoring dplyr methods
dplyr is active again:
palmerpenguins::penguins %>% # CAVEAT: factor columns are not supported yet mutate(across(where(is.factor), as.character)) %>% mutate(bill_area = bill_length_mm * bill_depth_mm) %>% summarize(.by = c(species, sex), mean_bill_area = mean(bill_area)) %>% filter(species != "Gentoo") #> # A tibble: 5 ร 3 #> species sex mean_bill_area #> <chr> <chr> <dbl> #> 1 Adelie male 770. #> 2 Adelie female 657. #> 3 Adelie NA NA #> 4 Chinstrap female 820. #> 5 Chinstrap male 984.
We would like to guide our efforts towards improving duckplyr, focusing on the features with the most impact. To this end, duckplyr collects and uploads telemetry data, but only if permitted by the user. The data collected contains:
- The package version
- The error message
- The operation being performed, and the arguments
- For the input data frames, only the structure is included (column types only), no column names or data
The first time the package encounters an unsupported function, data type, or operation, instructions are printed to the console.
palmerpenguins::penguins %>% as_duckplyr_df() %>% transmute(bill_area = bill_length_mm * bill_depth_mm) %>% head(3) #> The duckplyr package is configured to fall back to dplyr when it encounters an #> incompatibility. Fallback events can be collected and uploaded for analysis to #> guide future development. By default, no data will be collected or uploaded. #> โน A fallback situation just occurred. The following information would have been #> recorded: #> {"version":"0.3.1","message":"Can't convert columns of class <factor> to #> relational. Affected #> column:\n`...1`.","name":"transmute","x":{"...1":"factor","...2":"factor","...3":"numeric","...4":"numeric","...5":"integer","...6":"integer","...7":"factor","...8":"integer"},"args":{"dots":{"...9":"...3 #> * ...4"}}} #> โ Run `duckplyr::fallback_sitrep()` to review the current settings. #> โ Run `Sys.setenv(DUCKPLYR_FALLBACK_COLLECT = 1)` to enable fallback logging, #> and `Sys.setenv(DUCKPLYR_FALLBACK_VERBOSE = 1)` in addition to enable #> printing of fallback situations to the console. #> โ Run `duckplyr::fallback_review()` to review the available reports, and #> `duckplyr::fallback_upload()` to upload them. #> โน See `?duckplyr::fallback()` for details. #> โน This message will be displayed once every eight hours. #> materializing: #> --------------------- #> --- Relation Tree --- #> --------------------- #> Limit 3 #> r_dataframe_scan(0xdeadbeef) #> #> --------------------- #> -- Result Columns -- #> --------------------- #> - bill_area (DOUBLE) #> #> # A tibble: 3 ร 1 #> bill_area #> <dbl> #> 1 731. #> 2 687. #> 3 725.
This package also provides generics, for which other packages may then implement methods.
library(duckplyr) # Create a relational to be used by examples below new_dfrel <- function(x) { stopifnot(is.data.frame(x)) new_relational(list(x), class = "dfrel") } mtcars_rel <- new_dfrel(mtcars[1:5, 1:4]) # Example 1: return a data.frame rel_to_df.dfrel <- function(rel, ...) { unclass(rel)[[1]] } rel_to_df(mtcars_rel) #> mpg cyl disp hp #> Mazda RX4 21.0 6 160 110 #> Mazda RX4 Wag 21.0 6 160 110 #> Datsun 710 22.8 4 108 93 #> Hornet 4 Drive 21.4 6 258 110 #> Hornet Sportabout 18.7 8 360 175 # Example 2: A (random) filter rel_filter.dfrel <- function(rel, exprs, ...) { df <- unclass(rel)[[1]] # A real implementation would evaluate the predicates defined # by the exprs argument new_dfrel(df[sample.int(nrow(df), 3, replace = TRUE), ]) } rel_filter( mtcars_rel, list( relexpr_function( "gt", list(relexpr_reference("cyl"), relexpr_constant("6")) ) ) ) #> [[1]] #> mpg cyl disp hp #> Mazda RX4 Wag 21.0 6 160 110 #> Mazda RX4 Wag.1 21.0 6 160 110 #> Datsun 710 22.8 4 108 93 #> #> attr(,"class") #> [1] "dfrel" "relational" # Example 3: A custom projection rel_project.dfrel <- function(rel, exprs, ...) { df <- unclass(rel)[[1]] # A real implementation would evaluate the expressions defined # by the exprs argument new_dfrel(df[seq_len(min(3, ncol(df)))]) } rel_project( mtcars_rel, list(relexpr_reference("cyl"), relexpr_reference("disp")) ) #> [[1]] #> mpg cyl disp #> Mazda RX4 21.0 6 160 #> Mazda RX4 Wag 21.0 6 160 #> Datsun 710 22.8 4 108 #> Hornet 4 Drive 21.4 6 258 #> Hornet Sportabout 18.7 8 360 #> #> attr(,"class") #> [1] "dfrel" "relational" # Example 4: A custom ordering (eg, ascending by mpg) rel_order.dfrel <- function(rel, exprs, ...) { df <- unclass(rel)[[1]] # A real implementation would evaluate the expressions defined # by the exprs argument new_dfrel(df[order(df[[1]]), ]) } rel_order( mtcars_rel, list(relexpr_reference("mpg")) ) #> [[1]] #> mpg cyl disp hp #> Hornet Sportabout 18.7 8 360 175 #> Mazda RX4 21.0 6 160 110 #> Mazda RX4 Wag 21.0 6 160 110 #> Hornet 4 Drive 21.4 6 258 110 #> Datsun 710 22.8 4 108 93 #> #> attr(,"class") #> [1] "dfrel" "relational" # Example 5: A custom join rel_join.dfrel <- function(left, right, conds, join, ...) { left_df <- unclass(left)[[1]] right_df <- unclass(right)[[1]] # A real implementation would evaluate the expressions # defined by the conds argument, # use different join types based on the join argument, # and implement the join itself instead of relaying to left_join(). new_dfrel(dplyr::left_join(left_df, right_df)) } rel_join(new_dfrel(data.frame(mpg = 21)), mtcars_rel) #> Joining with `by = join_by(mpg)` #> [[1]] #> mpg cyl disp hp #> 1 21 6 160 110 #> 2 21 6 160 110 #> #> attr(,"class") #> [1] "dfrel" "relational" # Example 6: Limit the maximum rows returned rel_limit.dfrel <- function(rel, n, ...) { df <- unclass(rel)[[1]] new_dfrel(df[seq_len(n), ]) } rel_limit(mtcars_rel, 3) #> [[1]] #> mpg cyl disp hp #> Mazda RX4 21.0 6 160 110 #> Mazda RX4 Wag 21.0 6 160 110 #> Datsun 710 22.8 4 108 93 #> #> attr(,"class") #> [1] "dfrel" "relational" # Example 7: Suppress duplicate rows # (ignoring row names) rel_distinct.dfrel <- function(rel, ...) { df <- unclass(rel)[[1]] new_dfrel(df[!duplicated(df), ]) } rel_distinct(new_dfrel(mtcars[1:3, 1:4])) #> [[1]] #> mpg cyl disp hp #> Mazda RX4 21.0 6 160 110 #> Datsun 710 22.8 4 108 93 #> #> attr(,"class") #> [1] "dfrel" "relational" # Example 8: Return column names rel_names.dfrel <- function(rel, ...) { df <- unclass(rel)[[1]] names(df) } rel_names(mtcars_rel) #> [1] "mpg" "cyl" "disp" "hp"