> by(iris[,1:4] , Species , mean)

Species: setosa
[1] NA
------------------------------------------------------------
Species: versicolor
[1] NA
------------------------------------------------------------
Species: virginica
[1] NA
Warning messages:
1: In mean.default(data[x, , drop = FALSE], ...) :
  argument is not numeric or logical: returning NA

2: In mean.default(data[x, , drop = FALSE], ...) :
  argument is not numeric or logical: returning NA

3: In mean.default(data[x, , drop = FALSE], ...) :
  argument is not numeric or logical: returning NA

R> mean(iris[iris$Species == "setosa", 1:4])
[1] NA
Warning message:
In mean.default(iris[iris$Species == "setosa", 1:4]) :
  argument is not numeric or logical: returning NA

R> by(iris[,1] , iris$Species , mean)
iris$Species: setosa
[1] 5.006
------------------------------------------------------------
iris$Species: versicolor
[1] 5.936
------------------------------------------------------------
iris$Species: virginica
[1] 6.588

R> by(iris[,1:4] , iris$Species , colMeans)
iris$Species: setosa
Sepal.Length  Sepal.Width Petal.Length  Petal.Width
       5.006        3.428        1.462        0.246
------------------------------------------------------------
iris$Species: versicolor
Sepal.Length  Sepal.Width Petal.Length  Petal.Width
       5.936        2.770        4.260        1.326
------------------------------------------------------------
iris$Species: virginica
Sepal.Length  Sepal.Width Petal.Length  Petal.Width
       6.588        2.974        5.552        2.026

foo <- function(x, ...) sapply(x, mean, ...)
by(iris[, 1:4], iris$Species, foo)

R> by(iris[, 1:4], iris$Species, foo)
iris$Species: setosa
Sepal.Length  Sepal.Width Petal.Length  Petal.Width
       5.006        3.428        1.462        0.246
------------------------------------------------------------
iris$Species: versicolor
Sepal.Length  Sepal.Width Petal.Length  Petal.Width
       5.936        2.770        4.260        1.326
------------------------------------------------------------
iris$Species: virginica
Sepal.Length  Sepal.Width Petal.Length  Petal.Width
       6.588        2.974        5.552        2.026

R> with(iris, aggregate(iris[,1:4], list(Species = Species), FUN = mean))
     Species Sepal.Length Sepal.Width Petal.Length Petal.Width
1     setosa        5.006       3.428        1.462       0.246
2 versicolor        5.936       2.770        4.260       1.326
3  virginica        6.588       2.974        5.552       2.026