From a data frame, is there a easy way to aggregate (sum, mean, max et c) multiple variables simultaneously?

Below are some sample data:

library(lubridate)
days = 365*2
date = seq(as.Date("2000-01-01"), length = days, by = "day")
year = year(date)
month = month(date)
x1 = cumsum(rnorm(days, 0.05)) 
x2 = cumsum(rnorm(days, 0.05))
df1 = data.frame(date, year, month, x1, x2)

I would like to simultaneously aggregate the x1 and x2 variables from the df2 data frame by year and month. The following code aggregates the x1 variable, but is it also possible to simultaneously aggregate the x2 variable?

### aggregate variables by year month
df2=aggregate(x1 ~ year+month, data=df1, sum, na.rm=TRUE)
head(df2)

Solution 1

Yes, in your formula, you can cbind the numeric variables to be aggregated:

aggregate(cbind(x1, x2) ~ year + month, data = df1, sum, na.rm = TRUE)
   year month         x1          x2
1  2000     1   7.862002   -7.469298
2  2001     1 276.758209  474.384252
3  2000     2  13.122369 -128.122613
...
23 2000    12  63.436507  449.794454
24 2001    12 999.472226  922.726589

See ?aggregate, the formula argument and the examples.

Solution 2

With the dplyr package, you can use summarise_all, summarise_at or summarise_if functions to aggregate multiple variables simultaneously. For the example dataset you can do this as follows:

library(dplyr)
# summarising all non-grouping variables
df2 <- df1 %>% group_by(year, month) %>% summarise_all(sum)

# summarising a specific set of non-grouping variables
df2 <- df1 %>% group_by(year, month) %>% summarise_at(vars(x1, x2), sum)
df2 <- df1 %>% group_by(year, month) %>% summarise_at(vars(-date), sum)

# summarising a specific set of non-grouping variables using select_helpers
# see ?select_helpers for more options
df2 <- df1 %>% group_by(year, month) %>% summarise_at(vars(starts_with('x')), sum)
df2 <- df1 %>% group_by(year, month) %>% summarise_at(vars(matches('.*[0-9]')), sum)

# summarising a specific set of non-grouping variables based on condition (class)
df2 <- df1 %>% group_by(year, month) %>% summarise_if(is.numeric, sum)

The result of the latter two options:

    year month        x1         x2
   <dbl> <dbl>     <dbl>      <dbl>
1   2000     1 -73.58134  -92.78595
2   2000     2 -57.81334 -152.36983
3   2000     3 122.68758  153.55243
4   2000     4 450.24980  285.56374
5   2000     5 678.37867  384.42888
6   2000     6 792.68696  530.28694
7   2000     7 908.58795  452.31222
8   2000     8 710.69928  719.35225
9   2000     9 725.06079  914.93687
10  2000    10 770.60304  863.39337
# ... with 14 more rows

Note: summarise_each is deprecated in favor of summarise_all, summarise_at and summarise_if.


As mentioned in my comment above, you can also use the recast function from the reshape2-package:

library(reshape2)
recast(df1, year + month ~ variable, sum, id.var = c("date", "year", "month"))

which will give you the same result.

Solution 3

Using the data.table package, which is fast (useful for larger datasets)

https://github.com/Rdatatable/data.table/wiki

library(data.table)
df2 <- setDT(df1)[, lapply(.SD, sum), by=.(year, month), .SDcols=c("x1","x2")]
setDF(df2) # convert back to dataframe

Using the plyr package

require(plyr)
df2 <- ddply(df1, c("year", "month"), function(x) colSums(x[c("x1", "x2")]))

Using summarize() from the Hmisc package (column headings are messy in my example though)

# need to detach plyr because plyr and Hmisc both have a summarize()
detach(package:plyr)
require(Hmisc)
df2 <- with(df1, summarize( cbind(x1, x2), by=llist(year, month), FUN=colSums))

Solution 4

Where is this year() function from?

You could also use the reshape2 package for this task:

require(reshape2)
df_melt <- melt(df1, id = c("date", "year", "month"))
dcast(df_melt, year + month ~ variable, sum)
#  year month         x1           x2
1  2000     1  -80.83405 -224.9540159
2  2000     2 -223.76331 -288.2418017
3  2000     3 -188.83930 -481.5601913
4  2000     4 -197.47797 -473.7137420
5  2000     5 -259.07928 -372.4563522

Solution 5

Interestingly, base R aggregate's data.frame method is not showcased here, above the formula interface is used, so for completeness:

aggregate(
  x = df1[c("x1", "x2")],
  by = df1[c("year", "month")],
  FUN = sum, na.rm = TRUE
)

More generic use of aggregate's data.frame method:

Since we are providing a

  • data.frame as x and
  • a list (data.frame is also a list) as by, this is very useful if we need to use it in a dynamic manner, e.g. using other columns to be aggregated and to aggregate by is very simple
  • also with custom-made aggregation functions

For example like so:

colsToAggregate <- c("x1")
aggregateBy <- c("year", "month")
dummyaggfun <- function(v, na.rm = TRUE) {
  c(sum = sum(v, na.rm = na.rm), mean = mean(v, na.rm = na.rm))
}

aggregate(df1[colsToAggregate], by = df1[aggregateBy], FUN = dummyaggfun)

Solution 6

With the dplyr version >= 1.0.0, we can also use summarise to apply function on multiple columns with across

library(dplyr)
df1 %>% 
    group_by(year, month) %>%
    summarise(across(starts_with('x'), sum))
# A tibble: 24 x 4
# Groups:   year [2]
#    year month     x1     x2
#   <dbl> <dbl>  <dbl>  <dbl>
# 1  2000     1   11.7  52.9 
# 2  2000     2  -74.1 126.  
# 3  2000     3 -132.  149.  
# 4  2000     4 -130.    4.12
# 5  2000     5  -91.6 -55.9 
# 6  2000     6  179.   73.7 
# 7  2000     7   95.0 409.  
# 8  2000     8  255.  283.  
# 9  2000     9  489.  331.  
#10  2000    10  719.  305.  
#  with 14 more rows

Solution 7

For a more flexible and faster approach to data aggregation, check out the collap function in the collapse R package available on CRAN:

library(collapse)
# Simple aggregation with one function
head(collap(df1, x1 + x2 ~ year + month, fmean))

  year month        x1        x2
1 2000     1 -1.217984  4.008534
2 2000     2 -1.117777 11.460301
3 2000     3  5.552706  8.621904
4 2000     4  4.238889 22.382953
5 2000     5  3.124566 39.982799
6 2000     6 -1.415203 48.252283

# Customized: Aggregate columns with different functions
head(collap(df1, x1 + x2 ~ year + month, 
      custom = list(fmean = c("x1", "x2"), fmedian = "x2")))

  year month  fmean.x1  fmean.x2 fmedian.x2
1 2000     1 -1.217984  4.008534   3.266968
2 2000     2 -1.117777 11.460301  11.563387
3 2000     3  5.552706  8.621904   8.506329
4 2000     4  4.238889 22.382953  20.796205
5 2000     5  3.124566 39.982799  39.919145
6 2000     6 -1.415203 48.252283  48.653926

# You can also apply multiple functions to all columns
head(collap(df1, x1 + x2 ~ year + month, list(fmean, fmin, fmax)))

  year month  fmean.x1    fmin.x1  fmax.x1  fmean.x2   fmin.x2  fmax.x2
1 2000     1 -1.217984 -4.2460775 1.245649  4.008534 -1.720181 10.47825
2 2000     2 -1.117777 -5.0081858 3.330872 11.460301  9.111287 13.86184
3 2000     3  5.552706  0.1193369 9.464760  8.621904  6.807443 11.54485
4 2000     4  4.238889  0.8723805 8.627637 22.382953 11.515753 31.66365
5 2000     5  3.124566 -1.5985090 7.341478 39.982799 31.957653 46.13732
6 2000     6 -1.415203 -4.6072295 2.655084 48.252283 42.809211 52.31309

# When you do that, you can also return the data in a long format
head(collap(df1, x1 + x2 ~ year + month, list(fmean, fmin, fmax), return = "long"))

  Function year month        x1        x2
1    fmean 2000     1 -1.217984  4.008534
2    fmean 2000     2 -1.117777 11.460301
3    fmean 2000     3  5.552706  8.621904
4    fmean 2000     4  4.238889 22.382953
5    fmean 2000     5  3.124566 39.982799
6    fmean 2000     6 -1.415203 48.252283

Note: You can use base functions like mean, max etc. with collap, but fmean, fmax etc. are C++ based grouped functions offered in the collapse package which are significantly faster (i.e. the performance on large data aggregations is the same as data.table while providing greater flexibility, and these fast grouped functions can also be used without collap).

Note2: collap also supports flexible multitype data aggregation, which you can of course do using the custom argument, but you can also apply functions to numeric and non-numeric columns in a semi-automated way:

# wlddev is a data set of World Bank Indicators provided in the collapse package
head(wlddev)

      country iso3c       date year decade     region     income  OECD PCGDP LIFEEX GINI       ODA
1 Afghanistan   AFG 1961-01-01 1960   1960 South Asia Low income FALSE    NA 32.292   NA 114440000
2 Afghanistan   AFG 1962-01-01 1961   1960 South Asia Low income FALSE    NA 32.742   NA 233350000
3 Afghanistan   AFG 1963-01-01 1962   1960 South Asia Low income FALSE    NA 33.185   NA 114880000
4 Afghanistan   AFG 1964-01-01 1963   1960 South Asia Low income FALSE    NA 33.624   NA 236450000
5 Afghanistan   AFG 1965-01-01 1964   1960 South Asia Low income FALSE    NA 34.060   NA 302480000
6 Afghanistan   AFG 1966-01-01 1965   1960 South Asia Low income FALSE    NA 34.495   NA 370250000

# This aggregates the data, applying the mean to numeric and the statistical mode to categorical columns
head(collap(wlddev, ~ iso3c + decade, FUN = fmean, catFUN = fmode))

  country iso3c       date   year decade                     region      income  OECD    PCGDP   LIFEEX GINI      ODA
1   Aruba   ABW 1961-01-01 1962.5   1960 Latin America & Caribbean  High income FALSE       NA 66.58583   NA       NA
2   Aruba   ABW 1967-01-01 1970.0   1970 Latin America & Caribbean  High income FALSE       NA 69.14178   NA       NA
3   Aruba   ABW 1976-01-01 1980.0   1980 Latin America & Caribbean  High income FALSE       NA 72.17600   NA 33630000
4   Aruba   ABW 1987-01-01 1990.0   1990 Latin America & Caribbean  High income FALSE 23677.09 73.45356   NA 41563333
5   Aruba   ABW 1996-01-01 2000.0   2000 Latin America & Caribbean  High income FALSE 26766.93 73.85773   NA 19857000
6   Aruba   ABW 2007-01-01 2010.0   2010 Latin America & Caribbean  High income FALSE 25238.80 75.01078   NA       NA

# Note that by default (argument keep.col.order = TRUE) the column order is also preserved

Solution 8

Below is another way to summarize multiple columns, especially useful when the function needs further arguments. You can select all columns via everything() or a subset of columns like any_of(c("a", "b")).

library(dplyr)
# toy data
df <- tibble(a = sample(c(NA, 5:7), 30, replace = TRUE), 
             b = sample(c(NA, 1:5), 30, replace = TRUE), 
             c = sample(1:5, 30, replace = TRUE), 
             grp = sample(1:3, 30, replace = TRUE))
df
#> # A tibble: 30 × 4
#>        a     b     c   grp
#>    <int> <int> <int> <int>
#>  1     7     1     3     1
#>  2     7     4     4     2
#>  3     5     1     3     3
#>  4     7    NA     3     2
#>  5     7     2     5     2
#>  6     7     4     4     2
#>  7     7    NA     3     3
#>  8    NA     5     4     1
#>  9     5     1     1     2
#> 10    NA     3     1     2
#> #  with 20 more rows
df %>% 
  group_by(grp) %>%
  summarise(across(everything(), 
                   list(mean = ~mean(., na.rm = TRUE),
                        q75 = ~quantile(., probs = .75, na.rm = TRUE))))
#> # A tibble: 3 × 7
#>     grp a_mean a_q75 b_mean b_q75 c_mean c_q75
#>   <int>  <dbl> <dbl>  <dbl> <dbl>  <dbl> <dbl>
#> 1     1   6.6      7   2.88  4.25   3        4
#> 2     2   6.33     7   2.62  3.25   2.9      4
#> 3     3   5.78     6   3.33  4      3.09     4

Solution 9

Late to the party, but recently found another way to get the summary statistics.

library(psych) describe(data)

Will output: mean, min, max, standard deviation, n, standard error, kurtosis, skewness, median, and range for each variable.