3

How do I group by columns, then compute the mean and standard deviation of every other column in R?

As an example, consider the famous Iris data set. I want to do something similar to grouping by species, then compute the mean and sd of the petal/sepal length/width measurements. I know that this has something to do with split-apply-combine, but I am not sure how to proceed from there.

What I can come up with:

require(plyr)

x <- ddply(iris, .(Species), summarise,
    Sepal.Length.Mean = mean(Sepal.Length),
    Sepal.Length.Sd = sd(Sepal.Length),
    Sepal.Width.Mean = mean(Sepal.Width),
    Sepal.Width.Sd = sd(Sepal.Width),
    Petal.Length.Mean = mean(Petal.Length),
    Petal.Length.Sd = sd(Petal.Length),
    Petal.Width.Mean = mean(Petal.Width),
    Petal.Width.Sd = sd(Petal.Width))

     Species Sepal.Length.Mean Sepal.Length.Sd Sepal.Width.Mean Sepal.Width.Sd
1     setosa             5.006       0.3524897            3.428      0.3790644
2 versicolor             5.936       0.5161711            2.770      0.3137983
3  virginica             6.588       0.6358796            2.974      0.3224966
  Petal.Length.Mean Petal.Length.Sd Petal.Width.Mean Petal.Width.Sd
1             1.462       0.1736640            0.246      0.1053856
2             4.260       0.4699110            1.326      0.1977527
3             5.552       0.5518947            2.026      0.2746501

Desired output:

z <- data.frame(setosa = c(5.006, 0.3524897, 3.428, 0.3790644,
                           1.462, 0.1736640, 0.246, 0.1053856),
                versicolor = c(5.936, 0.5161711, 2.770, 0.3137983,
                               4.260, 0.4699110, 1.326, 0.1977527),
                virginica = c(6.588, 0.6358796, 2.974, 0.3225966,
                              5.552, 0.5518947, 2.026, 0.2746501))
rownames(z) <- c('Sepal.Length.Mean', 'Sepal.Length.Sd',
                 'Sepal.Width.Mean', 'Sepal.Width.Sd',
                 'Petal.Length.Mean', 'Petal.Length.Sd',
                 'Petal.Width.Mean', 'Petal.Width.Sd')
                     setosa versicolor virginica
Sepal.Length.Mean 5.0060000  5.9360000 6.5880000
Sepal.Length.Sd   0.3524897  0.5161711 0.6358796
Sepal.Width.Mean  3.4280000  2.7700000 2.9740000
Sepal.Width.Sd    0.3790644  0.3137983 0.3225966
Petal.Length.Mean 1.4620000  4.2600000 5.5520000
Petal.Length.Sd   0.1736640  0.4699110 0.5518947
Petal.Width.Mean  0.2460000  1.3260000 2.0260000
Petal.Width.Sd    0.1053856  0.1977527 0.2746501
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  • I think the value of the cell "setosa"/"Sepal.Length.Mean" should be 5.006, not 0.5006 in the "desired output" (looks like a typo). I will edit the question to fix this if nobody opposes – R Yoda May 26 '16 at 21:24

4 Answers4

9

We can try with dplyr

library(dplyr)
res <- iris %>% 
         group_by(Species) %>% 
         summarise_each(funs(mean, sd))
`colnames<-`(t(res[-1]), as.character(res$Species))
#                     setosa versicolor virginica
#Sepal.Length_mean 5.0060000  5.9360000 6.5880000
#Sepal.Width_mean  3.4280000  2.7700000 2.9740000
#Petal.Length_mean 1.4620000  4.2600000 5.5520000
#Petal.Width_mean  0.2460000  1.3260000 2.0260000
#Sepal.Length_sd   0.3524897  0.5161711 0.6358796
#Sepal.Width_sd    0.3790644  0.3137983 0.3224966
#Petal.Length_sd   0.1736640  0.4699110 0.5518947
#Petal.Width_sd    0.1053856  0.1977527 0.2746501

Or as @Steven Beaupre mentioned in the comments, the output can be obtained by reshaping with spread

library(tidyr)
iris %>% 
   group_by(Species) %>% 
   summarise_each(funs(mean, sd)) %>% 
   gather(key, value, -Species) %>% 
   spread(Species, value)
akrun
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    To avoid the matrix transpose, you could do: `iris %>% group_by(Species) %>% summarise_each(funs(mean, sd)) %>% gather(key, value, -Species) %>% spread(Species, value)` – Steven Beaupré May 26 '16 at 10:25
3

Here is the traditional plyr approach. It uses colwise to compute summary statistics on all columns.

means <- ddply(iris, .(Species), colwise(mean))
sds <- ddply(iris, .(Species), colwise(sd))
merge(means, sds, by = "Species", suffixes = c(".mean", ".sd"))
Richie Cotton
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1

If you want to use data.table for performance reasons you could try this (don't be afraid - more comments than code ;-) I have tried to optimize all performance critical spots.

library(data.table)
dt <- as.data.table(iris)

# Helper function similar to "colwise" of package "plyr":
# Apply a function "func" to each column of the data.table "data"
# and append the "suffix" string to the result column name.
colwise.dt <- function( data, func, suffix )
{
  result <- lapply(data, func)                                      # apply the function to each column of the data table
  setDT(result)                                                     # convert the result list into a data table efficiently ("by ref")
  setnames(result, names(result), paste0(names(result), suffix))    # append suffix to each column name efficiently ("by ref"). "setnames" requires a data.table
}

wide.result <- dt[, c(colwise.dt(.SD, mean, ".mean"), colwise.dt(.SD, sd, ".sd")), by=.(Species)]
# Note: .SD is a data.table containing the subset of dt's data for each group (Species), excluding any columns used in "by" (here: Species column)

# Now transpose the result
long.result <- melt(wide.result, id.vars="Species")

# Now transform into one column per group
final.result <- dcast(long.result, variable ~ Species)

wide.result is:

      Species Sepal.Length.mean Sepal.Width.mean Petal.Length.mean Petal.Width.mean Sepal.Length.sd Sepal.Width.sd Petal.Length.sd Petal.Width.sd
1:     setosa             5.006            3.428             1.462            0.246       0.3524897      0.3790644       0.1736640      0.1053856
2: versicolor             5.936            2.770             4.260            1.326       0.5161711      0.3137983       0.4699110      0.1977527
3:  virginica             6.588            2.974             5.552            2.026       0.6358796      0.3224966       0.5518947      0.2746501

long.result is:

       Species          variable     value
 1:     setosa Sepal.Length.mean 5.0060000
 2: versicolor Sepal.Length.mean 5.9360000
 3:  virginica Sepal.Length.mean 6.5880000
 4:     setosa  Sepal.Width.mean 3.4280000
 5: versicolor  Sepal.Width.mean 2.7700000
 6:  virginica  Sepal.Width.mean 2.9740000
 7:     setosa Petal.Length.mean 1.4620000
 8: versicolor Petal.Length.mean 4.2600000
 9:  virginica Petal.Length.mean 5.5520000
10:     setosa  Petal.Width.mean 0.2460000
11: versicolor  Petal.Width.mean 1.3260000
12:  virginica  Petal.Width.mean 2.0260000
13:     setosa   Sepal.Length.sd 0.3524897
14: versicolor   Sepal.Length.sd 0.5161711
15:  virginica   Sepal.Length.sd 0.6358796
16:     setosa    Sepal.Width.sd 0.3790644
17: versicolor    Sepal.Width.sd 0.3137983
18:  virginica    Sepal.Width.sd 0.3224966
19:     setosa   Petal.Length.sd 0.1736640
20: versicolor   Petal.Length.sd 0.4699110
21:  virginica   Petal.Length.sd 0.5518947
22:     setosa    Petal.Width.sd 0.1053856
23: versicolor    Petal.Width.sd 0.1977527
24:  virginica    Petal.Width.sd 0.2746501

final.result is:

            variable    setosa versicolor virginica
1: Sepal.Length.mean 5.0060000  5.9360000 6.5880000
2:  Sepal.Width.mean 3.4280000  2.7700000 2.9740000
3: Petal.Length.mean 1.4620000  4.2600000 5.5520000
4:  Petal.Width.mean 0.2460000  1.3260000 2.0260000
5:   Sepal.Length.sd 0.3524897  0.5161711 0.6358796
6:    Sepal.Width.sd 0.3790644  0.3137983 0.3224966
7:   Petal.Length.sd 0.1736640  0.4699110 0.5518947
8:    Petal.Width.sd 0.1053856  0.1977527 0.2746501

The only difference to your desired output is the final results contains the value names in the first column named variable instead of storing this in the row names. This could be done by setting the row names to the first column and removing the first column...

R Yoda
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1

Inspired by the answers, I figured out a solution that also works, using only dplyr and tidyr functions.

require(tidyr)
require(dplyr)

x <- iris %>%
    gather(var, value, -Species)
print(tbl_df(x))

# Compute the mean and sd for each dimension
x <- x %>%
    group_by(Species, var) %>%
    summarise(mean = mean(value), sd = sd(value)) %>%
    ungroup
print(tbl_df(x))

# Convert the data frame from wide form to long form
x <- x %>%
    gather(stat, value, mean:sd)
print(tbl_df(x))

# Combine the variables "var" and "stat" into a single variable
x <- x %>%
    unite(var, var, stat, sep = '.')
print(tbl_df(x))

# Convert the data frame from long form to wide form
x <- x %>%
    spread(Species, value)
print(tbl_df(x))
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