Aggregate multiple rows of the same data.frame in R based on common values in given columns

aggregate(value ~ item + size + weight, FUN = mean, data=df)

  item size weight value
1    B    1      2     3
2    C    3      2     1
3    A    2      3     5

Here is the solution using the ddply from plyr package:

library(plyr)
ddply(df,.(item),colwise(mean))
  item size weight value
1    A    2      3     5
2    B    1      2     3
3    C    3      2     1

df$value <- ave(df$value,df$item,FUN=mean)
df[!duplicated(df$item),]

  item size weight value
1    A    2      3     5
3    B    1      2     3
4    C    3      2     1