Summarizing multiple columns with dplyr? [duplicate]

Question

In dplyr (>=1.00) you may use across(everything() in summarise to apply a function to all variables:

library(dplyr)

df %>% group_by(grp) %>% summarise(across(everything(), list(mean)))
#> # A tibble: 3 x 5
#>     grp     a     b     c     d
#>   <int> <dbl> <dbl> <dbl> <dbl>
#> 1     1  3.08  2.98  2.98  2.91
#> 2     2  3.03  3.04  2.97  2.87
#> 3     3  2.85  2.95  2.95  3.06

Alternatively, the purrrlyr package provides the same functionality:

library(purrrlyr)
df %>% slice_rows("grp") %>% dmap(mean)
#> # A tibble: 3 x 5
#>     grp     a     b     c     d
#>   <int> <dbl> <dbl> <dbl> <dbl>
#> 1     1  3.08  2.98  2.98  2.91
#> 2     2  3.03  3.04  2.97  2.87
#> 3     3  2.85  2.95  2.95  3.06

Also don't forget about data.table (use keyby to sort sort groups):

library(data.table)
setDT(df)[, lapply(.SD, mean), keyby = grp]
#>    grp        a        b        c        d
#> 1:   1 3.079412 2.979412 2.979412 2.914706
#> 2:   2 3.029126 3.038835 2.967638 2.873786
#> 3:   3 2.854701 2.948718 2.951567 3.062678

Let's try to compare performance.

library(dplyr)
library(purrrlyr)
library(data.table)
library(bench)
set.seed(123)
n <- 10000
df <- data.frame(
  a = sample(1:5, n, replace = TRUE), 
  b = sample(1:5, n, replace = TRUE), 
  c = sample(1:5, n, replace = TRUE), 
  d = sample(1:5, n, replace = TRUE), 
  grp = sample(1:3, n, replace = TRUE)
)
dt <- setDT(df)
mark(
  dplyr = df %>% group_by(grp) %>% summarise(across(everything(), list(mean))),
  purrrlyr = df %>% slice_rows("grp") %>% dmap(mean),
  data.table = dt[, lapply(.SD, mean), keyby = grp],
  check = FALSE
)
#> # A tibble: 3 x 6
#>   expression      min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 dplyr        2.81ms   2.85ms      328.        NA     17.3
#> 2 purrrlyr     7.96ms   8.04ms      123.        NA     24.5
#> 3 data.table 596.33µs 707.91µs     1409.        NA     10.3

We can summarize by using summarize_at, summarize_all and summarize_if on dplyr 0.7.4. We can set the multiple columns and functions by using vars and funs argument as below code. The left-hand side of funs formula is assigned to suffix of summarized vars. In the dplyr 0.7.4, summarise_each(and mutate_each) is already deprecated, so we cannot use these functions.

options(scipen = 100, dplyr.width = Inf, dplyr.print_max = Inf)

library(dplyr)
packageVersion("dplyr")
# [1] ‘0.7.4’

set.seed(123)
df <- data_frame(
  a = sample(1:5, 10, replace=T), 
  b = sample(1:5, 10, replace=T), 
  c = sample(1:5, 10, replace=T), 
  d = sample(1:5, 10, replace=T), 
  grp = as.character(sample(1:3, 10, replace=T)) # For convenience, specify character type
)

df %>% group_by(grp) %>% 
  summarise_each(.vars = letters[1:4],
                 .funs = c(mean="mean"))
# `summarise_each()` is deprecated.
# Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
# To map `funs` over a selection of variables, use `summarise_at()`
# Error: Strings must match column names. Unknown columns: mean

You should change to the following code. The following codes all have the same result.

# summarise_at
df %>% group_by(grp) %>% 
  summarise_at(.vars = letters[1:4],
               .funs = c(mean="mean"))

df %>% group_by(grp) %>% 
  summarise_at(.vars = names(.)[1:4],
               .funs = c(mean="mean"))

df %>% group_by(grp) %>% 
  summarise_at(.vars = vars(a,b,c,d),
               .funs = c(mean="mean"))

# summarise_all
df %>% group_by(grp) %>% 
  summarise_all(.funs = c(mean="mean"))

# summarise_if
df %>% group_by(grp) %>% 
  summarise_if(.predicate = function(x) is.numeric(x),
               .funs = funs(mean="mean"))
# A tibble: 3 x 5
# grp a_mean b_mean c_mean d_mean
# <chr>  <dbl>  <dbl>  <dbl>  <dbl>
# 1     1   2.80   3.00    3.6   3.00
# 2     2   4.25   2.75    4.0   3.75
# 3     3   3.00   5.00    1.0   2.00

You can also have multiple functions.

df %>% group_by(grp) %>% 
  summarise_at(.vars = letters[1:2],
               .funs = c(Mean="mean", Sd="sd"))
# A tibble: 3 x 5
# grp a_Mean b_Mean      a_Sd     b_Sd
# <chr>  <dbl>  <dbl>     <dbl>    <dbl>
# 1     1   2.80   3.00 1.4832397 1.870829
# 2     2   4.25   2.75 0.9574271 1.258306
# 3     3   3.00   5.00        NA       NA

You can simply pass more arguments to summarise:

df %>% group_by(grp) %>% summarise(mean(a), mean(b), mean(c), mean(d))

Source: local data frame [3 x 5]

  grp  mean(a)  mean(b)  mean(c) mean(d)
1   1 2.500000 3.500000 2.000000     3.0
2   2 3.800000 3.200000 3.200000     2.8
3   3 3.666667 3.333333 2.333333     3.0

For completeness: with dplyr v0.2 ddply with colwise will also do this:

> ddply(df, .(grp), colwise(mean))
  grp        a    b        c        d
1   1 4.333333 4.00 1.000000 2.000000
2   2 2.000000 2.75 2.750000 2.750000
3   3 3.000000 4.00 4.333333 3.666667

but it is slower, at least in this case:

> microbenchmark(ddply(df, .(grp), colwise(mean)), 
                  df %>% group_by(grp) %>% summarise_each(funs(mean)))
Unit: milliseconds
                                            expr      min       lq     mean
                ddply(df, .(grp), colwise(mean))     3.278002 3.331744 3.533835
 df %>% group_by(grp) %>% summarise_each(funs(mean)) 1.001789 1.031528 1.109337

   median       uq      max neval
 3.353633 3.378089 7.592209   100
 1.121954 1.133428 2.292216   100