Better Grouped Summaries in dplyr
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For R
dplyr
users one of the promises of the new rlang
/tidyeval
system is an improved ability to program over dplyr
itself. In particular to add new verbs that encapsulate previously compound steps into better self-documenting atomic steps.
Let’s take a look at this capability.
First let’s start dplyr
.
suppressPackageStartupMessages(library("dplyr")) packageVersion("dplyr")
## [1] '0.7.1.9000'
A dplyr
pattern that I have seen used often is the “group_by() %>% mutate()
” pattern. This historically has been shorthand for a “group_by() %>% summarize()
” followed by a join()
. It is easiest to show by example.
The following code:
mtcars %>% group_by(cyl, gear) %>% mutate(group_mean_mpg = mean(mpg), group_mean_disp = mean(disp)) %>% select(cyl, gear, mpg, disp, group_mean_mpg, group_mean_disp) %>% head()
## # A tibble: 6 x 6 ## # Groups: cyl, gear [4] ## cyl gear mpg disp group_mean_mpg group_mean_disp ## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 6 4 21.0 160 19.750 163.8000 ## 2 6 4 21.0 160 19.750 163.8000 ## 3 4 4 22.8 108 26.925 102.6250 ## 4 6 3 21.4 258 19.750 241.5000 ## 5 8 3 18.7 360 15.050 357.6167 ## 6 6 3 18.1 225 19.750 241.5000
is taken to be shorthand for:
mtcars %>% group_by(cyl, gear) %>% summarize(group_mean_mpg = mean(mpg), group_mean_disp = mean(disp)) %>% left_join(mtcars, ., by = c('cyl', 'gear')) %>% select(cyl, gear, mpg, disp, group_mean_mpg, group_mean_disp) %>% head()
## cyl gear mpg disp group_mean_mpg group_mean_disp ## 1 6 4 21.0 160 19.750 163.8000 ## 2 6 4 21.0 160 19.750 163.8000 ## 3 4 4 22.8 108 26.925 102.6250 ## 4 6 3 21.4 258 19.750 241.5000 ## 5 8 3 18.7 360 15.050 357.6167 ## 6 6 3 18.1 225 19.750 241.5000
The advantages of the shorthand are:
- The analyst only has to specify the grouping column once.
- The data (
mtcars
) enters the pipeline only once. - The analyst doesn’t have to start thinking about joins immediately.
Frankly I’ve never liked the shorthand. I feel it is a “magic extra” that a new user would have no way of anticipating from common use of group_by()
and summarize()
. I very much like the idea of wrapping this important common use case into a single verb. Adjoining “windowed” or group-calculated columns is a common and important step in analysis, and well worth having its own verb.
Below is our attempt at elevating this pattern into a packaged verb.
#' Simulate the group_by/mutate pattern with an explicit summarize and join. #' #' Group a data frame by the groupingVars and compute user summaries on #' this data frame (user summaries specified in ...), then join these new #' columns back into the original data and return to the user. #' This works around https://github.com/tidyverse/dplyr/issues/2960 . #' And it is a demonstration of a higher-order dplyr verb. #' Author: John Mount, Win-Vector LLC. #' #' @param d data.frame #' @param groupingVars character vector of column names to group by. #' @param ... list of dplyr::mutate() expressions. #' @value d with grouped summaries added as extra columns #' #' @examples #' #' add_group_summaries(mtcars, #' c("cyl", "gear"), #' group_mean_mpg = mean(mpg), #' group_mean_disp = mean(disp)) %>% #' head() #' #' @export #' add_group_summaries <- function(d, groupingVars, ...) { # convert char vector into quosure vector # These interfaces are still changing, so take care. groupingQuos <- lapply(groupingVars, function(si) { quo(!!as.name(si)) }) dg <- group_by(d, !!!groupingQuos) ds <- summarize(dg, ...) ds <- ungroup(ds) left_join(d, ds, by= groupingVars) }
This works as follows:
mtcars %>% add_group_summaries(c("cyl", "gear"), group_mean_mpg = mean(mpg), group_mean_disp = mean(disp)) %>% select(cyl, gear, mpg, disp, group_mean_mpg, group_mean_disp) %>% head()
## cyl gear mpg disp group_mean_mpg group_mean_disp ## 1 6 4 21.0 160 19.750 163.8000 ## 2 6 4 21.0 160 19.750 163.8000 ## 3 4 4 22.8 108 26.925 102.6250 ## 4 6 3 21.4 258 19.750 241.5000 ## 5 8 3 18.7 360 15.050 357.6167 ## 6 6 3 18.1 225 19.750 241.5000
And this also works on database-backed dplyr
data (which the shorthand currently does not, please see dplyr
2887 issue and dplyr
issue 2960).
con <- DBI::dbConnect(RSQLite::SQLite(), ":memory:") copy_to(con, mtcars) mtcars2 <- tbl(con, "mtcars") mtcars2 %>% group_by(cyl, gear) %>% mutate(group_mean_mpg = mean(mpg), group_mean_disp = mean(disp))
## Error: Window function `avg()` is not supported by this database
mtcars2 %>% add_group_summaries(c("cyl", "gear"), group_mean_mpg = mean(mpg), group_mean_disp = mean(disp)) %>% select(cyl, gear, mpg, disp, group_mean_mpg, group_mean_disp) %>% head()
## # Source: lazy query [?? x 6] ## # Database: sqlite 3.19.3 [:memory:] ## cyl gear mpg disp group_mean_mpg group_mean_disp ## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 6 4 21.0 160 19.750 163.8000 ## 2 6 4 21.0 160 19.750 163.8000 ## 3 4 4 22.8 108 26.925 102.6250 ## 4 6 3 21.4 258 19.750 241.5000 ## 5 8 3 18.7 360 15.050 357.6167 ## 6 6 3 18.1 225 19.750 241.5000
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